Yes, it will be a free update.Will it be a free upgrade for existing users? I won't lie, but I got a bit annoyed having to pay again to go from 3>5 when 3 broke due to OS X changes.
Most of the ones that will need big updates use hacks (e.g. menucracker) which have long been discouraged by Apple and are finally being forced out. I would expect that many apps which have been following the rules will be just fine or have minor tweaks to take advantage of some OS X improvements.If any of my apps need a paid update to work, El Capitan can kiss my a**