There is an audio book/story called "The Second Oil Age". It has a pretty neat weapon called "the squid gun". It is mainly for incapacitation, rather than killing - it fires a blob of some sticky (non-living) material that also wraps around the target with several tentacle like elongations. If fired in the face it will quickly lead to asphyxiation as it's VERY hard to remove, especially in time to prevent death. It's an idea to look into. The description should be in the third episode (can't find a transcript unfortunately).

Blaster rifle used by Rebel Alliance in Star Wars capable of melting Storm Troopers but otherwise reflected by every inanimate objects and of course plot armour. ;D

Neutron bombs? Gravity weapons? Though starships should have shielding as standard. Then there's always science fantasy tech like Xenosaga with UMN weapons, or transporter sniper rifles in Star Trek, that fire through another layer of reality thereby circumventing barriers and distance in this one.

@DKNguyen Neutrons were also the first thing I thought of when I saw the question title. Although, as you suggested, if we're talking "futuristic science fiction," then there could be weapons using tricks that don't (yet) exist in the real world, but were carefully tailored to meet the needs of the plot . . .

@Lorendiac Psyker powers. Thalaron radiation.

How about weaponized music?

I'm reminded of Larry Niven's Neutron Star in which a character has to investigate the deaths of some scientists who were investigating a neutron star inside a (supposedly) impenetrable starship hull. Turns out there is one thing that can penetrate the hull...

You might look at high energy protons. In proton therapy, different proton velocities will deposit their energies at different tissue depths. Some variation of this might work for your story.

Why don't you buy your ship hulls from General Products instead?

US Navy veteran here. I know you want sci-fi, but in matters of practicality, the answer finally depends on the energy economy of your sci-fi. If energy is cheap enough, hulls WOULD be 'orders-of-magnitude' thicker, because a ship that can be sabotaged by a 22-caliber pistol can't go to war. I could completely empty an M-16 into a submarine hull and the only thing that will happen is people will shoot back, and maybe a prison sentence supposing I survive. Personal armor would not survive a similar assault.

Radio broadcast something into the ships PA system, and you kill the ship's crew without damaging the hull ... EDIT: I see that @Renan had a similar idea (though I would have expected Kate Bush)

@SeanBoddy The difference between a submarine hull and a spacecraft hull is that a submarine is designed to keep the pressure out, where the pressure difference can be much greater than 1 atmosphere which requires a very strong hull. A spacecraft is designed to keep a pressure of less than one atmosphere in, which doesn't require a thick hull.

Bring back swords! Traveller was right (Traveller was the first SF RPG, and the Marines were taught the use of the cutlass of all things).

Honestly just immobilising them and throwing them out of an airlock seems like the safest option, pretty much anything that can pass through armour can damage ship-equipment (even radiation/electrical based weapons are risky)

True story: Civil war-era submarine, depth charge set off near it (underwater). Submarine basically OK, but crew crushed to jelly due to the shockwave generated inside the hull.

@NomadMaker, my point is that it depends on his energy economy. Think Star Trek; energy is cheap and abundant, therefore they build hulls that can withstand significant damage. The reasons they use phasers instead of bullets aboard ship is they fire line-of-sight, can be reliably made non-lethal, and energy is cheap and abundant. World building decisions have consequences - energy economy is a huge, fundamental piece of every other decision, including ships' hulls.

"Unless the answer is that ships all have hulls that are an order of magnitude thicker than anything a human could actually wear." That is the answer. today, why do you think it would be any different in the future?

If you board an enemy ship, and you're not wearing a pressure suit, they can simply close bulkheads between you and them, then open an airlock between you and space. You asphyxiate and battle is over. This simple strategy means the only reasonable boarding strategy is to wear pressure suits. Which means during battle, no one is going to care if the ship de-pressurizes via bullet holes. Bullet holes in the hull would simply be patched after the battle.

Also no one is going to trade more risk of dying for the reward of maybe having to repair the ship a little less later. Soldiers would wear pressurized armor and use whatever weapon is most effective at keeping them alive and the fastest method for making the enemy dead. Collateral damage is a concern for after the life-or-death melee is over.