These are more like frond end Questions so it may depend on the on the launcher you use
Myself I have yet to hit a limit and I know of no front end that let you use multiple paths that I know of anyway, but not updated my loader in some time either
The only limit I ever hit was the 500 Wii games per partition
EDIT I suppose you could have another launcher for different Nands but for me I just installed everything to a single nand, though off the top of my head I am not sure I set myself any limits or just installed all the official Wads
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