WMD's often look and feel powerful in movies. Powerful things, often big but sometimes small to offset for it's incredibly destructive capabilities launched at each other.
But the true danger can be much faster and invisible. Whether it's computer viruses or biological, both are incredibly dangerous on spaceships.
The computer virus can take control of one or multiple systems, either crippling them, removing control or giving control to someone else. Doors, lights, oxygen, navigation. The options are numerous. You might tear the ship apart by activating all boosters in opposite directions, or pressurise one cabin and depressurise another, and opening a door in between. Poison the air or lock them out. Short circuit or underpower systems. Depending on your goal it's versatile both for story purposes as well as for the crews goals.
The second one is biological. Much more difficult in space battles, but not unimaginable. If you can somehow spike the enemy ship, you can already win. The space version of VX nerve gas, a bacteria that'll eat them from the inside and avoid electronics, a virus that'll simply kill them or a cordiceps fungi that controls them to open up all the airlocks.
AI is incredibly dangerous, allowing you to have a mathematical edge if it's better than another. This can help with navigation, targeting and automation. Potentially you just put van Neumann bots at work, attacking a ship and using the materials and energy to make more of itself until the target(s) are destroyed.
There is one very good WMD in space. EMP. Spaceships might be shielded, but only up to a certain amount. Setting off a significant EMP next to a spaceship can render them inoperable, leaving the crew floating in the dark in an increasingly deteriorating ship. Turning off systems as they do in movies isn't very effective against this.
You can also go for the "normal" explosive and kinetic route to WMD's. That is just putting enough of a certain amount of energy on your target. Physical, heat, electrical or whatever. If you put too much of it on your target you're generally golden. The only way is to deliver it. Potentially you can just use a lot of lasers pointed at the exact right spot, instantly heating it to a degree that it'll weaken too much. Then your WMD power is mostly calculation.