Terrain deformations have a separate handle count. Basically any handle you create will remain in memory until removed or destroyed. Some don't have destroy/remove functions (such as trackables or terrain deformations--they stay in memory for the entire map's length).
A few handles are not tracked on the regular handle stack, and therefore they won't show up on the handle count. This includes text tags, weather effects, lightning, and a few others.
All in all, just make sure you check your triggers. A lot of fps lag is just because of graphic strain (particle-intense effects, many units, etc.). It won't necessarily be because of leaks. The handle count method is a good way to check for leaks, but it won't always show you what you want, especially because of the way the handle stack behaves. Just leak-proof your triggers and you should be fine. 1000 or 2000 leaks won't make significant performance hit on your map (unless perhaps it occurs all at once, but it will be just a quick lag spike), so remember that you have leeway.