I've been wondering about this! Does Spanish regularly form diminutives other than with the -it- infix? ("m'hijito" etc.) Latin forms them with -ill-, -cul-, or -ul-, and many such forms are obvious in Spanish (tomatillo / quesadilla etc.), but I've never known whether -ill- is still productive today or if those are relics from the past.
It's fun to see a Spanish region bordering Portugal (-inho) forming diminutives with -iño and one bordering France (-ette) forming them with -ete.
And indeed I see this on etymonline:
> from Latin nucleus "kernel," from nucula "little nut," diminutive of nux (genitive nucis) "nut,"
So for whatever reason a new word was called for, and our nucleus comes from that, not from the diminutive form of "nut".