I'm not a big fan of the "Don't Sweat The Small Stuff" mantra because what's small to someone else might be huge to me. But that's not really the issue...
Since the goody bags and shirt sound really cool, don't punish the little boy by not giving it to him - it's not his fault his mom can't take him, and it does sound like he really wanted to come. Still give it to him and let him enjoy it. Having four active kids of my own and husband who travels more often than not, I know it's really hard to juggle being everywhere with everyone...which is why you do ask for favors from people. Maybe your friend knows someone who can bring her son. Since you are the host of the party, it's probably not realistic for her to drop off the child to you early because you will be in party prep mode, but maybe there is another friend...
Since the goody bags and shirt sound really cool, don't punish the little boy by not giving it to him - it's not his fault his mom can't take him, and it does sound like he really wanted to come. Still give it to him and let him enjoy it. Having four active kids of my own and husband who travels more often than not, I know it's really hard to juggle being everywhere with everyone...which is why you do ask for favors from people. Maybe your friend knows someone who can bring her son. Since you are the host of the party, it's probably not realistic for her to drop off the child to you early because you will be in party prep mode, but maybe there is another friend...

I have to give a final count 2 days before the party so I gave myself a buffer in case anyone forgets and calls late. I do have to pay per head though so I can sympathize with the OP on her disappointment. But I do think that life happens and if it were me and I already had some type of personal treat bag made for the child I'd make sure he got it to make him feel good. One of my friends will be out of town for dd's party and her dh is going to be bringing him. I told her though that her ds was more than welcome to stay with us or we could even pick him up if she needed us to in order to make it easier on her dh. I know she really appreciated that.
