yes, the gunk that usually gets down into the gravel will most likely just rest on top of the sand. you can hover the vac over the sand and pick that stuff up.
as for the bacteria...i've done full substrate changes a couple of times before, fish still in tank and never bothered keeping any of the old substrate in to seed the new gravel. your filtration system is where the biggest majority of benefecial bacteria is stored so as long as nothing messes up your filtration you should be fine. as has already been said, if you just want to be extra cautious then by all means, there's nothing wrong witih that but imo it's not necessary.
one thing that I haven't seen mentioned yet but you've probably already thought of anyway, but just in case, if your filter has an adjustable flow rate, then I would reduce it as much as possible while you're adding the sand just to keep it from sucking up any more floating particles than necessary.
also you could empty the tank then put the sand in and poor the water onto a plate, that should reduce the amount the sand gets churned which will reduce clowdiness