For several years, and several boats, I've done the following (keeping in mind that many pumps come apart for cleaning and need "head room"):
1) Dried and cleaned with mineral spirits an area in the bilge about 2 times the footprint of the pump ( for ease of installation later). Make sure there is enough "head room" to take the pump apart for cleaning in the area you've picked.
2) Sand cleaned hull area with 20 grip sand paper
3) Lightly sand bottom of bilge pump base with 20 grit sandpaper enough to leave visible, even, scratching
4) Apply even coat (about 1/4" thick) of Life Seal ( or equivalent silicone and polyurethane sealant ) over base of bilge pump insuring that a very small amount fills the mounting holes in the base of the pump with a VERY small mushroom on the inside ( working side) of the pump.
An alternative solution, is to remotely mount a diaphragm style pump with a hose inlet and a remote pickup. these pickups are usually only an inch or so in height.
5) Firmly press pump into center of the cleaned and sanded hull area taking care that the orientation of the pumps outlet hose is where you want it to be. I've had a slightly better experience taking the pump apart ( snapping off the removable pump housing from its base) and installing the base in the sealant sans the pump itself.
6) When full cure time has ended ( see instructions on product) reassemble pump. ( this is where you will find out if you did all of step #1 correctly.
Pump base is removable if necessary with a putty knife and a moderate amount of force.
I've used this on both my boats, one of which is a deep V that is often run in Barnegat Bay's pincushion chop "at speed".
Alternatively, remotely mount a diaphragm style bilge pump with a hose inlet, with a remote pickup in the bilge. These pickups are usually only an inch or so in height. Caution should be used using the seal approach with this style pickup since the ones I've seen are open base and the sealant would need to be applied carefully. These bases usually bronze which also will need to be roughened for sealant to adhere.
