It can make a difference to the sound. I once had a Squier Affinity Tele that had a top-loading bridge. It certainly had a different sound and feel to another Squier Tele with a rear-loading bridge (even with similar replacement pickups). Fender themselves swapped to a top-loading bridge back in 1959 for a short while (it's obviously a cheaper construction method), but swapped back at some point in 1960 to rear-loading due to complaints from their users.
There is nothing inherently wrong with top-loading bridges on Teles, it's just different (though with the cast alloy block saddles on my Squier they were very difficult to re-string) and you will get some players who prefer them. But I prefer the longer sustain that a rear-loading bridge gives. I've noticed a big difference in that on a couple of my bases which provide both options.
