Yes they do
count - an AS is designed to be exactly half of an A level. In the UMS (Unified Mark Scheme) an AS is out of 300, an A2 another 300 so the final A level grade is based on total scores out of 600. The exact conversion of exam marks to UMS varies widely, and different modules are worth different UMS scores -
http://www.suttcold.bham.sch.uk/Website ... grades.pdf
Retakes (usually in January of Yr 13) are possible to improve the overall final mark but universities will probably have already seen the initial AS grades and might very well make offer decisions accordingly.