multiple reasons for me:
booties are very swampy to wear in warm weather (wet, hot, humid, etc) - so they aren't really an option here in 91* water
since i will be in /around water for 6 - 10 hours, i want my feet (and pants, and gloves) as dry as possible- i find (some) water shoes drain well - however they all suck at preventing little rocks and shells from getting in. then some of these particles find their way onto the tramp, and then ... on your knees
i have found bootie sole's don't hold up well with all the stops/walks we do in our sailing (we race island to island and then hang out for a bit
we have lots of sharp oysters around here - and other sea shells. I have seen (had) them go right through bootie soles
the booties i used to use in winter sailing required a support team to remove at the end of the day - and my team all quit - i no longer sail unless its 65* and sunny. I have a dry bib for when the gulf gets to a brisk temp.