GoldenEye is a FPS, conkers and fur day is a incredibly crude game involving a giant turd who sings about how he's going to throw his shit at you.
The age rating raise isn't really relevant. Nintendo has been down for high aged rating games for a long time, which is how things like eternal darkness, Geist, bayonettas, or the fatal frame collaboration games came about. But conker isn't the same as those games. It's the exact kind of content that there's no chance in hell Nintendo wants to be associated with. Even if they had never sold rare, they'd still not want it tied to them. Even if they had the opportunity to release it, they wouldn't want to.
And calling it beloved is vastly overselling it. GoldenEye was an actual beloved genre defining game, and conker is in no way comparable. GoldenEye ended up as a multimillion seller. Do you know how many copies bad fur day sold? Final numbers aren't easy to find, but it was below 100k, making it one of the biggest flops in Nintendo history. The only claim to fame it has is basically as "we can't believe Nintendo let this release"
This is all well and good, but let's not forget that Nintendo is the company that let
Conker's Bad Fur Day exist and release in the first place - they had plenty enough sway at Rare in the late 90's to get the game cancelled if they didn't want to have anything to do with it. A sequel had even been apparently greenlit, before getting cancelled upon the Microsoft buyout of Rare.
And while
Conker didn't exactly set the charts on fire, that doesn't mean it wasn't beloved - it was highly rated by critics at the time, both for its humour and its gameplay and it is still looked back on fondly as well. Yes,
Goldeneye sold way better than it and was inordinately more influential than it;
Goldeneye also sold more than every other N64 game barring two and also better than 90% of the things Nintendo has already put on NSO across all platforms - I don't think
Jelly Boy or
S.C.A.T. or the GBC version of
Alone in the Dark did amazingly sales wise either. Just because one thing was bigger and more beloved, doesn't mean that the smaller, niche thing wasn't also beloved.
I doubt I'll sway you but, I don't think
Conker being very crude is enough to stop Nintendo from wanting it on NSO, and I don't think it being a commercial failure really matters - Nintendo wouldn't be just selling
Conker, they're selling a whole service of which
Conker could be a part of
(commercial viability would've been more of a concern back when they still did the Virtual Console model tbf). Sure maybe it'd not be enough of a pull by itself to get Nintendo to make a deal for it, but my thought has always been that they've done a deal to get the Rare games together; with
Banjo-Kazooie and
Goldeneye merely being the headline titles brought out earlier due to being the best selling two.
Anyways, if it happens it happens - if it doesn't, oh well.