As people say; it's how you manage wet feet, and the socks and footwear you use that can avoid such problems.
When I first did it years ago , on longer trips I used to get underfoot blisters due to one area of hard skin under my forefoot softening due to being constantly wet.
Just like with any footwear choice for any situation/usage, in this case, once I understood my own feet's reaction to being wet, and how various socks, shoes and footbeds interact; I could prepare and manage better, and it was no longer much of a problem. No more than any footwear choice.
Everything needs dialling in?
The "feel" of wet feet to me is only uncomfortable if something is wrong with my setup. Just like the feel of dry feet can be uncomfortable if something is wrong with the shoe/sock/skin on my feet.