Going bare feet is definitely quieter then with boots. That also makes sense though, so i wouldn't change that.
The only thing i miss is that bare feet don't have disadvantages to compensate, while in real live it does. There is a reason people wear shoes, because going bare feet could hurt if you step on something that is in the sand/dirt (like rocks, twigs, etc.) and also if you walk over wood (splinters). I think going bare feet and stepping on rocks or twigs/branches should do a tiny bit of damage and temporarely slow you down for about maybe 3 seconds and on the ships you should have a small chance of getting that same thing due to splinters from the wooden deck.