You probably have to understand that this was still the 1980s when this deal was signed and Nintendo was still a fly-by-their-pants "small" company that wasn't run as "professionally" as a global corporation would be today. The Nintendo of today was not the Nintendo of then.
The deal with Sony for CD-ROM tech was signed in 1988, they really only hit the big time with the Famicom around 1984/85, before that, they were a small time arcade company that hit pay dirt with Donkey Kong and previous to that they were all over the map making various products.
They probably did not properly vet the deal and just looked at NEC making a CD drive for the PC Engine and Sega working on one for the upcoming Mega Drive and figured they better sign something too.
Nintendo was kind of "wild" in those days, like Yamauchi for example cancelled the Game Boy and they only released it because the Super Famicom got delayed from 1989 into 1990. Otherwise there would be no Game Boy, believe it or not. The industry was way, way different back then it was much more like the wild west.
In hindsight, Nintendo should have just let Sony release their Super NES CD-drive, let it fizzle out and die as pretty much every console add-on did back in those days and then made sure to redraw the terms for their next system a lot more carefully.