Let's consider the case however many cards are in your deck.
There's two orders you could resolve in: if you resolve the Watchtower first, you may trash the Inn, or put the Inn on your deck where it already was because of Develop, then you resolve the Inn which requires you to shuffle your deck (even if you don't choose any action cards to shuffle in), leaving you either with a trashed Inn (and a shuffled deck, which may or may not happen before you topdeck the other card gained by Develop, since Develop lets you choose the order) or an Inn somewhere in your deck (and again, the other card gained by Develop could be on top or shuffled in, you choose the order). Otherwise, you could resolve the Inn first, shuffling your deck, and then fail to resolve Watchtower due to lose track, leaving you with an Inn shuffled into your deck as before.
So, the options are: trash the Inn, or shuffle it into your deck; either way you have the other card either gained on top of your deck or shuffled in, your choice. I don't see where it matters that your deck has only one card; I guess it's an academic question of whether you can trash the Inn after you "shuffled it in" because you still know where it is, in which case the answer is probably no.