Even though some towers like the Banana Farm do not pop Bloons, they still have a pop count.
In the mobile version the Banana Farm doesn't have a pop count. Neither does the Monkey Village, which will get pop count if upgraded to High Energy Beacon though.
Before the 5.0 update in BTD6, the pop count increases with cash collected from Banana Farms or other money-making towers like Merchantmen.
This was replaced with a new "Cash Count" icon.
In Bloons Tower Defense 5 Mobile, the Pop Count counter becomes 0 when a tower gets upgraded. This also applies to Bloons Tower Defense Battles Mobile and Bloons Monkey City Mobile, but in both cases it becomes normal again when that tower pops a bloon or if the player exits the tower's menu and reopens it.