And the Logitech F310 costs even less to manufacture than wholesale. But a controller with an analogue stick would cost more to manufacture than one that is just moulded plastic with a circuit board and a rubber membrane inside it. If Nintendo were to make N64 controller for a Mini Console they would have to pay to re-engineer it, fire up a plant and build new moulds, and because it wasn't the most robust controller initially they would have to make a call on whether to stick true to the original design or risk 'affecting the purity' by say subbing in the more sturdy GC analouge stick (which some people do as a mod themselves). And this is all about the controller - still have to make the actual software and hardware.
Then Nintendo has to weigh up if all this R&D and manufacture cost is worth the potential sales. A Mini N64 would probably sell less than the NES or SNES variants and cost more to make. These mini consoles are built to a cost and to a particular RRP to maximise profit and with an N64 it just doesn't seem to be as an easy pay day. Plus, where's the NES and SNES can look okay on a modern day display, a lot of people are going to have their childhood memories shattered when they see a blurry, early 3D game running at 12fps on their giant screen a home.
Also, the Mini console boom may be over now and that's another thing Nintendo may have taken into consideration. The newly released Sega Mega Drive/Genesis was fantastic, especially after all the half-arsed efforts that were coming out from third parties until Sega finally gave a shit and did it themselves, but is already available in some places with a significant discount. And there was that recent thread about Konami being worried that the PC Engine mini console pre-orders have been weak (
https://www.neogaf.com/threads/rumor-pc-engine-mini-pre-orders-are-faring-very-poorly.1518463/unread). This I attribute to a lot of cowboy companies jumping on the mini console/tiny arcade machine band wagon and flooding the market with absolute garbage and now customers are more wary. Nobody needed dogshit like this running a single terrible old NES game;
So there probably won't be a Mini N64 anytime soon but that doesn't mean people won't be able to play it's great games. Be it remakes or emulation on newer home hardware (official or 'otherwise'), there will always be a way to make people tear their palms into bloody messes via Mario Party.