Does "how many cows" include heifers too ?

Yes.
This is actually a decision we struggled with.
Should "How many cows are in pen 4" include heifers ?
While we understand the difference, we decided yes - that we would consider "cows" to be a generic term, and "cows" means all animals.

If you want only adults, you can say "how many adults...".
If you want only  heifers, you can say "how many heifers...".

If you say "How many cows" or "How many animals" you'll get both adults and heifers listed.

If too many people complain about what "cows" means, we can reconsider this, or make it a setting.