The select clause is the last clause to be executed logically, except for order by. The having clause happens before select, so the aliases are not available yet.
If you really want to use an alias, not that I'd recommend doing this, an in-line view can be used to make the aliases available:
select StoreId, _count
from (select Store_id as StoreId, count(*) as _count
from StoreProduct
group by Store_id) T
where _count > 0
Or in SQL Server 2005 and above, a CTE:
; with T as (select Store_id as StoreId, count(*) as _count
from StoreProduct
group by Store_id)
select StoreId, _count
from T
where _count > 0