That's only my opinion..others will have their own.
Another opinion I hear get tossed around a lot is that he removed them himself to rid himself of mortal imperfections.
I have my own theory that he removed his flesh to attempt to "clone" himself like Divath Fyr did with his "girls", and that maybe there's a mad Sotha Sil clone running around out there somewhere, but that's really just my imagination being silly and overactive.
He is known to be one of the Psijic Order, a reclusive group of mages residing on a constantly-shifting island of the Summerset Isles. So maybe your right.
I'm sorta leaning towards the idea that TES:V will be set in summerset isles.
And if Fyr could do it i bet sotha sil could.
That would be so cool to have him in TES:V.