I'm sort of agreement with the rest. If you opt to keep your full load-out on your person, 24-7, then encumbrance penalties should probably apply.
If your ship is Small or Larger, you likely have a berth, bunk, rack or even quarters where you can stash sufficient gear to reduce your encumbrance, even if it's just the space under a hammock slung up in the cargo bay.
If your ship is a tiny, one or two-person ship, it may apply if your armor keeps you encumbered. Even a small fighter should have a small storage bay to hold a back-pack and few weapons. I can't see someone traipsing across the galaxy with a flame-thrower in your lap. I would also assume that powered armor could not be work while in control of such a craft.