Will owners of alien ships have a more difficult time sourcing materials and components to keep their ships operating correctly?
TL;DRAlien ship owners shouldn't struggle with parts, since components like a Tevarin shield can be swapped for human ones or upgraded, though rarer alien parts may need hunting down.
They shouldn't do. Especially in the case of the Banu ships, you should be able to fit in things like human items, or human-produced items, in there. So if your Tevarin shield goes bust, you won't necessarily have to fit a Tevarin shield back in there, but you'll be able to slot a human one in instead.
So the components that a ship comes with when we sell it in its concept are not necessarily the only components that you can equip in a ship. These are the items that the ship comes with initially, but you'll be able to swap out coolers, swap out power plants, swap out shields, and maybe even upgrade them. So while the cool Tevarin shield comes with it, and maybe the cool Xi'an engines come with it, you could possibly upgrade them to even better components, maybe even from different races or sources.
Yeah, you can upgrade, downgrade, sidegrade. The choice is yours, really. But I wouldn't recommend getting rid of the Tevarin shield. It'll be too good.
But yeah, it might also be where you're acquiring the alien ship. There's potential there for some parts to be... Like Jonny said, you could do a human equivalent, but maybe if you want to maintain that specific, harder-to-find part, you might have to venture out into the far reaches of the universe and hunt it down.