It depends on the hotel and who is at the desk if it will be a hassle or not. Most are OK with the spouses stay free, but some are pains with the breakfast coupons, even if you book for two.

I've never been leaving the EWR Hilton late enough to do the breakfast, but their check in people seem to have way more trouble then any other Hilton I've ever been with in getting things right, so if they hassle you remember it's not you, they hassle people all the time there, I think it chases their bordom away or something.