I am playing with the same idea on my 89 and 90 SP stable.
According to the experts I have been in contact with, physically it should be ok.
What I have found is that it is a little more difficult to find the newer bn38 from a single-carb installation and if you get a dual-carb setup with the intent of using just one of the carbs you will find, and I am still playing around for a solution, but will kinda hijack your thread to share some info/questions.
Note the dual-carb setups, one is stamped "mag" and the other is stamped "pto".
In the dual-carb setup, the one with the fuel pump has pretty much free-flow output on the return side that feeds the input on the other carb, the non-fuel pump carb has a much smaller return flow orifice, presumably so you maintain the same fuel pressure on both carbs. These orifice dimensions are described in SeaDoo specifications documents but seem to vary between models and I have not sat down to study it further yet.
My theory, being set up on a bench-run setting, is that you should be able to use the non-fuel-pump carb in a single-carb config using the external fuel pump that is in place now. This of course based on the sub-theory that the external and carb-mounted fuel pumps are designed to supply the same fuel pressure/flow.
My second theory is that you should be able to bypass the external fuel pump and use the fuel pump on the carb in a single-carb config. The problem that I am looking at resolving is what size orifice do I need in the return line to insure proper fuel pressure. In my limited experience and perusing stuff here it appears that newer skis use this method where the output lines from both carbs go to a "Y" fitting then to the return line to the fuel tank and little hints and logic indicate that the flow restriction in the output line(s) to maintain fuel pressure will either be in both carbs or in the return line back to the fuel tank.
Have I screwed with your mind enough or maybe even helped?
Calling experts ... help us out here ... or tell me that I should just go back out on my porch with a cold one and continue my rain cloud watch.