I've taken both routes. I've gone on a few trips where I have a regular pair hiking boots as well as a $20 pair of sandals for creek crossings. Lately I leave behind the sandals, and when it comes time to get wet I just take off my socks, take out the insoles, roll up/take off my pants, and let my shoes get soaked. So long as I don't do that often enough to get trenchfoot I think it's fine, and I don't mind if my shoes are a little squishy for a while.

It's also nice to have some sandals to switch into when at the campsite. If you choose to only have one set of footwear then you can just change into fresh socks and loosen up the laces.