Yes self checkout machines do take and accept $100.00 bills.
Just be aware that if you put $100.00 bill into the self checkout that it might not have enough change to give you back if your purchase is way less than $100.00
But if that happens you should let the self checkout attendant know about it so that they can help get you your change back.
I've used self checkout and paid with a $100.00 bill before for items that amounted to almost $100.00
But mostly I use a credit or debit card when shopping but if I do need to use a $100.00 bill to pay at self checkout then I will and it's worked out okay.