Murder and Metroid
My first Metroid game was Super Metroid, and I approached it much like I did most action-y games: anything that was even slightly threatening got hunted down and destroyed if possible. Most action-y games with a system conceptualized as combat encourage or outright demand a player hunt down and kill everything around, so this just seemed natural. There's something of a trend nowadays of games that push back against 'murder everything', such as how Dishonored adjusts the endgame in response to your willingness to kill and is pretty explicitly judgmental about murder throughout your play, but usually if a game doesn't explicitly make frowny-faces at the player over murder, the game is designed around 'kill everything that moves'.
Honestly, even many games that do frown at the player for murdering people are fundamentally designed under 'kill everything that moves', with the frowning being tacked on atop this core design principle fairly awkwardly. (Dishonored is somewhat guilty of this, in fact, with powers that are nearly useless or completely if you aren't willing to kill people and a tendency for map design to make stealth kills far more expedient for freeing up the player's options, though it's one of the better examples out there)
Unfortunately, I actually didn't play Super Metroid that much when I got it on the SNES originally. I got stick fairly early, unable to find Kraid, and it took more than two years for me to get access to a strategy guide to get an answer. (This being in the years before GameFAQs was the default answer when stuck) As such, I didn't get much of an opportunity to get a sense of the nuance in Super Metroid's design until later, when I came back to it after playing Prime and Fusion, so this story is a little convoluted.
Playing Prime and Fusion was a fairly shocking experience in a lot of ways. Fusion's design fairly rapidly disabused me of the notion that running around killing everything is the path to success: this is technically viable early in the game, and also viable in the endgame, but for most of the game Fusion punishes minor mistakes with 40+ Energy penalties, in a game where almost all enemies will provide 10 or maybe 20 Energy when killed. As such, getting into fights with everything you encounter is a way to rapidly burn through your Energy supply ie die horribly. I learned to pick and choose my battles, because most fights weren't worth pursuing. Once I started trying to beat the game in under 2 hours, this was exacerbated further: most enemies just take too long to kill if you're trying to get through the game quickly.
With Prime I persisted in going out of my way to pick fights with enemies. I did fairly quickly start ignoring enemies that were substantially out of my way and not actively pursuing me, such as the Flickerbats in Phendrana Drift's entrance area, but I remained fairly aggressive about hunting down and murdering anything that came after me or was even slightly in my way and possible for me to kill, especially if I could kill it without expending resources. (ie Missiles) It was only on what was probably literally my twentieth playthrough that it abruptly clicked that not only was this a thing I was doing, but that it was a thing that was actively inventing problems for me within the game's framework. It was actually this fairly farcical moment, wherein I had just killed a Plazmite for the millionth time, begun grumbling to myself about maneuvering in the darkness, and then stopped and realized that if I hadn't killed the Plazmite I wouldn't be wandering in the dark.
That was a bit of a lightbulb moment in general. After that, I played Prime with a different eye, specifically questioning whether it was really worth fighting a given enemy or group of enemies. As with Fusion, my attempts to get through the game faster and more efficiently accelerated this still further: it took a long time for me to start doing things like running right on past the Space Pirates in the entrance to the Phazon Mines, who would do little damage if I just kept moving, usually less than if I did bother to fight them.
Then, having played Prime and Fusion and in each case separately found myself pushed to not kill everything that moves, I went back to Super Metroid, and... what do you know, it mirrored my experiences with its future games, particularly Fusion's design. It was less obvious than with Fusion, since you can get decently-sized Energy drops in Super Metroid, but generally speaking in Super Metroid enemies just really are not worth the time and possible Energy loss to kill unless the game actually either explicitly mandates it (eg locking you into the room until everything is dead) or constructs the environment so that slipping past a given enemy without harm is much less practical than actually killing them.
That latter point leads nicely into a subtle element of the design common to all three -and indeed it is also found in Zero Mission, Echoes, classic Metroid, classic Metroid II, and to a lesser extent Corruption- wherein enemy design and environmental design is often deliberately designed so that most enemies are actually easier to avoid than to fight. Skree will land behind you and completely miss you if you just run right under them, and there's almost never another enemy actually placed in your way to make this unsafe. In general, if something is clearly conceived of as a wild animal, even if it's an aggressive animal, it's usually perfectly possible to avoid fighting it, and usually doing so is safer and faster than getting into a fight with it. (Prior to Screw Attack making basically everything trivial, anyway) A very memorable example is the Covern, which are quite spooky and spawn right on top of Samus... but then take so long to gain a hitbox or hurtbox that if you completely ignore them you'll probably never take any damage from them. The fact that they respawn unlimitedly also means that killing them is pointless: it won't ever get you safe. You've got to go find Phantoon and kill it to make them stop.
Meanwhile, and this is very interesting, Samus' actual enemies are much more likely to be placed as unavoidable obstacles: there's a particularly memorable region early in Super Metroid's upper Crateria where you encounter a series of Space Pirates in tunnels that are only very slightly taller than the enemies themselves. It's not possible to jump over them without touching them, or use the Morph Ball to slip under them. You basically have to either kill them or clip through them while taking damage, and the latter is fairly difficult to do in Super Metroid to boot, due to how you get pushed away from an enemy you touch and frequently Samus' invincibility frames will end by the time you manage to get back into contact with the enemy that originally hurt you.
The overall result is that it is technically an option to wander around and kill basically everything you see in a Metroid game, but it's not the smart thing to do.
It's interesting to me in part because some sections of the Metroid fandom like to characterize Samus as a fairly bloodthirsty individual who comes in and wipes out entire ecosystems, but if you're playing these games the way they encourage you to play, you end up playing a surprisingly compassionate warrior who largely avoids fighting the local wildlife, even the portion of it that goes out of its way to run her down, and focusing your ire on your actual enemies instead.
It's a startlingly nuanced and moral game design philosophy.