I know of a few people who have them at 90 deg, they never have said anything about it not flowing with the gases as being a problem with boost related issues, although ext/wastegate manufacturers always have disclaimers saying not to mount them in 90 deg configurations as it does not allow the gases to flow to the wastegate properly to control boost levels.
Suppose it all depends on what boost youll be pushing the tune of your engine and the mapping so i dont think it really matters if its at 90 deg we cant all live in a perfect world.