Pop Count is how many bloons a tower has popped. Super Monkeys and Spectres usually have the most because of their attack speed and popping power. Every layer of a bloon a tower pop adds one to the towers pop count. Every time a tower hits a Ceramic Bloon, M.O.A.B., B.F.B., or Z.O.M.G., that does not go to their pop count. However, if they get thier multi-hit layer destroyed completely, it does count and gives the Pop count equivalent to the multi-hit layer bloon's childern.
Even though some towers like the Banana Farm do not pop Bloons, they still have a pop count. It was problaby added by the developers.
In Bloons Tower Defense 5 Mobile, the Pop Count counter resets when a Tower gets upgraded. This also applies to Bloons Tower Defense Battles Mobile, even though in BTD Battles the pop count returns to normal after a couple seconds.