Can the mod count ghost tiles?

Yes. You can include ghost tiles in your counts by holding shift while making the selection using the GC selection tool. Tiles that are part of a blueprint that you're importing are automatically included in the ghost counts if that blueprint is in your inventory. Unfortunately, if the blueprint you're importing into the mod is from your blueprint library, tiles are not counted, because the modding API does not support it. Regular entities in those blueprints will still be counted though.

How does the mod keep track of ghosts?

Once you've used the selection tool to select an area containing ghost entities, the mod registers those entities with the game such that the game fires an event when they get "destroyed" (this includes when they get deleted or the entity they represent gets built). This means the mod only goes through the list of ghosts you're tracking a single time at the beginning to do the initial count and never again.

What does the mod's "Minimum update interval" map setting do?

The mod only updates its data and refreshes its GUI in response to relevant in-game events. When you have the mod window open, for example, the mod will listen for ghosts getting destroyed, as well as for changes in your inventory and your personal logistics in order to show accurate figures. Because many such events can take place within the same tick or in very short succession, the mod will not fully reprocess its data or update the GUI any more frequently than dictated by this setting. Increasing the value in this setting, will make the full data processing and GUI update happen less frequently, minimizing the associated performance cost.