You've misidentified the trade-off - it's not a choice between swappable batteries or waterproof devices - obviously either swappable or non-swappable devices can be designed to be waterproof.
The trade-off is usually size and complexity. You need more space for the seals (gaskets, O-rings etc.), and then latching mechanisms to hold covers on while applying the correct amount of pressure (and uniform pressure) on the gaskets.
That's not an especially hard an engineering problem, it just necessarily takes up more space so you end up with a bulkier device, which people tend not to like as much unless they really value being able to swap the battery.
It becomes an engineering problem when you are trying to make it small and light.
I recently replaced the battery in my chest strap heart rate monitor. And I found I was lucky--turns out the seal had slipped and it hadn't been waterproof since the last battery change.
And I think the sealing mechanism probably increases the device volume by 50%. As a chest strap that's not a big deal.
The trade-off is usually size and complexity. You need more space for the seals (gaskets, O-rings etc.), and then latching mechanisms to hold covers on while applying the correct amount of pressure (and uniform pressure) on the gaskets.
That's not an especially hard an engineering problem, it just necessarily takes up more space so you end up with a bulkier device, which people tend not to like as much unless they really value being able to swap the battery.