And it may have involved tradeoffs in terms of internal space, design, etc. that Apple weren't willing to make.
It's highly unlikely that this played a role in their decision.
Waterproofing the headphone jack isn't more complicated than waterproofing the charging port.
Not to mention, they replaced the headphone jack with even more holes which also require sealing.
There are plenty of waterproof phones with headphone jacks.