YABVU, and completely ridiculous to fall out with your brother over this
I will have to change my seating plan which has been printed as his name is on it.

That is so funny.
I have fallen out with my brother now tk the point where he is also now not coming to my wedding
Well how ridiculous are you?
Quite apart from the fact it isn't actually your brother's decision nor his fault, even if there were someway he could force him to come and sit sulky faced at missing his holiday, would you really want that?
This is your brother.
Who you have now stopped from coming.
Apart from the hurt that will cause for years to come, on a practical level, you now also have 2 people not coming rather than one. 
He has not apologised for my nephew not coming
I'm pretty sure somewhere in that chat he said "Sorry, sis, but ex has booked a holiday and ds is going with her so won't be able to come to your wedding"
or offered to help pay for him not being there
Eh ?
It isn't costing you more because he isn't there.
Quite aside from most caterers will let you firm numbers up to about 10 days before, and the fact you could ask someone else along, even if the seat is empty, you'd budgeted for him anyway, so it is a shame if it is wasted, but it isn't really costing you.
I am really disappointed with my nephew
He's 15. No 15 yr old is going to turn down a holiday to spend a day at a wedding. Be reasonable. This wedding is big for you, obviously, but not for other folk.
but I feel his Dad should put his foot down about it?
No, it is up to the 15 yr old. Shame the ex didn't take it into account and book the holiday a different time, but you can't blame your brother for that.
Am I blowing things out of proportion?
Yup. Completely.