On a company denying a guest appearance, it could happen. If Konami doesn't want Snake associated with Nintendo or its characters (because they are too kiddy maybe), then they will certainly do it. There could also be the situation where the company wants more money or they have an agreement with another company to keep a series off a platform. And rights can change. It's not as simple as you make it.
And no, you have to renew the license agreement to do that. Konami is not going to let you release a game with their properties without them having a say. Micheal Patcher discussed this in one of his videos (despite not being able to predict his way out of a paper bag, he knows a good deal about the inner workings of the industry). Long story short, the brand holder would get paid again. If not, the company could file an injunction and get the game recalled. Starts at about 7min
https://www.youtube.com/watch?v=scXqVfKKNvg
This is why I say Nintendo may move away from licensing as much as they have with Smash 5. That may not be the only reason (Iwata let Sakurai do whatever he wants and Kimishima may reign it in for numerous reasons). I could be wrong on that. I have been in the past, but I say this because people tend to go in the complete opposite direction and say everyone under the sun will be in Smash. There is more going on behind the scenes.
What I will say is hold on to a copy of Super Smash Bros for Wii U. With so many licensed characters in that game and it's lower sales, you'll never see a re-release of that game. Keep it. It will be worth a lot of money in the future.
NonSpecificGuy
I covered what you mentioned above, so I guess you can consider this a reply to your post too. Only thing I'll add is that if the licensed was timed, it would have run out by now/ Brawl is almost 10 years old so even if it covered future releases, they'd have to renew.