In many typical exhaust systems the water lift
sends the water up to a high spot where it then slopes down gradually until being discharged.
As David says the back pressure can be an issue, but typically it is the height from the water lift
to the "high spot". If by raising the discharge it becomes higher than the higher spot than the pressure may be effected.
As Nick says, you can flood your engine, this really sucks.
The vertical distances of the various components in the exhaust system verses the waterline, are critical......, and don't imagine that the manufacturer got it right to start with.
When I re-powered I went on an extensive learning
spree to to engineer
my new system.