You should be concerned yes, because wet feet are not happy feet.
However, this is something your shoe manufacturer should have taken care of. I have owned Specialized and Lake brands of waterproof shoes. I have not ever had problems with water entering through the cleat holes of either (I have owned A LOT of Lake boots). However, that doesn't mean your manufacturers have the same care. You could call to inquire, or better yet, test.
It should be easy to stopper a sink and put the footbed below the waterline to see what happens. Testing one's equipment is a great way to build confidence in it.