What do you gain from having your NNID linked? I think it lets you use your eshop balance if you buy from a PC but I seem to accumulate gold and silver points just the same.
Linked NNID lets you use your eShop balance on 3DS and Wii U. It has nothing to do with being able to make digital Switch game purchases on Nintendo.com. It's because they moved to this new system when the Switch launched, they used the NNID linkage method to unify the old system used on 3DS and Wii U.