Having worked in Merchandise, yes, the stores will be open. Some of the smaller ones may not be due to staffing, but the bigger stores will definately be open, especially along the Main Midway, which is also your best bet for finding all varieties of shirts. Pagoda has a few, Park Plaza (right next to the Demon Drop) has most of them including polos, and you can find most tshirts at other small stores along the Midway.
A tip I'd recommend is find the shirt you want earlier in the day and know which stores have it in the right size, so you don't have to go looking around that late. That way, you'll be able to ride late but get right to the shirt! If all else fails, the shops in Hotel Breakers (go in the front door and all the way to the back of the lobby) have all the shirts as well, and stay open later than the park.
-------------
PO!NT OF VIEW - A Different Look at Roller Coasters
http://www.crosswinds.net/~justmayntz/thrills/