As asked in the topic title.

Ship upgrades are separate items. You "install" them by putting those items into the fitting slot in the ship management UI. Thus, you can "uninstall" those items again by removing them from the slot back into your stash. You can then install them on another ship. 

So yes: they can be transferred.

Only exception: there are (very few) special ships you can possibly gain via story progression which can't be upgraded nor will the special items they have (like a special hull or something) can't get uninstalled. 

But for every ship you will buy it will work.

1 hour ago, Boeroer said:

Only exception: there are (very few) special ships you can possibly gain via story progression which can't be upgraded nor will the special items they have (like a special hull or something) can't get uninstalled.

You use the plural. I know of one, but are there really more than one?

I couldn't remember what's going on with upgrades with the RDC vessel (only used that once) so I played it safe.

Also cosmetic stuff, like animal hold and nice captains quarters don't transfer. It's in the description.

Thanks.