I think an important clarification is needed here: "at the same time, especially lategame". Clearing 3 players over the course of the game in a typical 10:3 is not only not harmful, it's about the expected number (or even a little less than the expected number) for a game to be balanced.
However, the reason that this is balanced is that if a player is cleared enough, scum can normally just kill them before town get more clears and dominate the game. Having a number of clears exceeding the number of scum at lylo is an obvious, and not very interesting, town victory. If you're running a 10:3 and three of your players are intended to be cleared by night mechanics, you should make those clears happen in different ways at different times, so that by the time the game reaches, say, a 3:2 ending, there's only one fully cleared and one circumstantially cleared player left.
Also bear in mind that players can be cleared by setup speculation too. I normally aim for about one player cleared by setup speculation and three cleared by role mechanics when I'm balancing a 10:3. (This might seem massively townsided to players who aren't used to balancing setups, but experience shows that something like that is necessary.)