In the process of routing a course to take advantage of the best natural features on a property, if the last hole ends up being a par 3, so be it. That's what I say!
By altering a solid routing to avoid a par 3 18th, the potential quality of the course in question would undoubtedly be sacrificed.
Off the top of my head, I can think of two Stanley Thompson layouts with par 3 eighteenth holes: 1) Ladies Golf Club of Toronto, and 2) Oshawa Golf Club. [Although, come to think of it, Thompson might have inherited the routing at Oshawa. Nonetheless...]
The 18th at Ladies GC, which sits right next to one of the classiest clubhouses (circa mid 1920s) I've ever seen, is excellent: an uphill shot of medium length to a semi-blind putting surface surrounded by bunkers. It's a really simple hole, that's equally cool... it's probably the best hole on the course in fact.
Toronto's Scarboro G&CC (remodelled by Tillighast in the early 1930s) has a par 3 19th hole, which is fun to finish on... as long as you win the bet, of course