For Hamilton, try the Admiral Inn (York and Dundurn near the 403 exit). Someone else mentioned they have a $40 day rate and no I.D. required..
For Stoney Creek, try the Cherry Beach Motel located on the North Service Rd in between Centennial Parkway and Fruitland Rd exits off the QEW. $35 day rate if you check-in b4 6pm, and probably no I.D. required.
There are quite a few places on Plains Rd, Burlington, but you might have to pay $20 more to have the escort delivered there. I've had good luck with the Bell Motel.