Really curious - which Apps rely on the Headphone jack? And how would they be unrecovered by changing to the Lightning port?
Personally, I can think of only one that might present a problem, and I believe the enclosed, free, Lightning to 3.5mm Headphone jack will circumvent that problem. That single problem would be the SquareD Visa/Mastercard reader. But, as I'm sure that this has been considered, I doubt that whatever problem you imagine will be a problem; is either has been fixed, or will be fixed in an update coming out soon. App developers do not want to lose sales, because Apple made an updated iPhone. As a developer - I know I wouldn't want to lose any sales, so I am certainly going to keep to date on my apps. I would assume they would too.
I have a guitar amp simulator called Amp Kit+ which has a ton of add on programs and it has a hardware kit that attaches to the headphone jack. Because of the delay that is inherent in blue tooth (as much as 700ms) you have to use the headphone jack. Even with that there is a software delay.
I actually use the program with my older 4S phone so I don't kill the battery on my 6S.
Additionally I have some blue tooth headphones, but the batteries are always dying just when you need them.