They keep their host clean and free from stuff like lice or fleas (bonus to resist disease)
They help repair damage their host sustains (Faster healing/regeneration?)
Same benefits for any of the gear they regularly wear/carry, as those represent outlying colonies
Their structures are durable, and provide additional damage resistance
You can upgrade the bonuses they give you by advancing their civilization's tech level. Get a bonus to spot from teams of observers with tiny telescopes on watch 24/7. Get bonuses on knowledge checks from scholars educated in universities. Bonuses on crafting things with fine detail from crews of architects and excavators who etch and alter your workpiece at a scale you can barely even see.
Maybe you can improve their military too, have them stage an invasion of your target by initiating a grapple. From that point on your opponent gets status effects and possibly even ongoing damage.
Downsides include civic unrest, rebellion, holy wars, separatists, all the other things that can cause a tiny civilization to be thrown into turmoil. Can you imagine your backpack declaring itself a sovriegn nation?