You dont really need to worry about them, delete them all they are still yours you just download again.
There are apps that wont transfer from ipad to ipod (but very few)
so if you dont want to clear any space, from ipad just eave it alone, when you buy your ipod (same itunes account?) just go to app store and download the apps you want (you wont be charged for apps you have already bought)
the behaviour suggests that aps you are buying are not getting added to itunes as well look for the "purchased" tab in itunes.
bare in mind this is jus tthe app, doesnt always copy data within the app