I ride in either trainers or a pair of German ex-army boots I picked up from the surplus store, it depends on the weather and what I'm doing at Uni that day.
I've never had any issues with the boots movement wise and they reach about a third to almost half way up my shin., the only difference I do notice is that the sole is much thicker, so the first time I used them it felt weird and almost floaty as my feet weren't going where they normally go when I pedal.
Conversely last time I played with the fit of my bike, I was wearing my boots, so when I got on it next with my trainers my seat was a tiny bit too high.