I'm pretty sure i'm not reaching here and i will explain why:
@Green_vs_Red:
I don't exactly know why either character was included but they weren't included for any special reason. Other than Sakurai just being weird and unpredictable with his roster selections.
Duck hunt dog was planned from the very begining of Smash 4 development in order to represent that era of gaming. Skaurai stated this in an interview. They had a specific purpose other than relevancy. The ice climbers were the same, added in order to have a veteran rep and Pit eventually got the same treatment in brawl. Mr. G&W and R.O.B. as what would be the final two characters are more so for surprise but their relevancy to nintendo as a company is not just a passing factor.
Earthbound had came out about 6 years prior to Smash 64 so Ness wasn't that relevant. Captain Falcon to his credit had a game that had come out about a year prior to Smash 64 but not that relevant imo.
There are two things you need to think here. The first is how many Nintendo IP had sequels in japan that they could draw characters from (at this time). To my knowledge only Pilotwings, excitebike, fire emblem and famicom wars fit this category and were not in smash 64. Out of these i would argue fire emblem is the only one with proper representation. However Fire emblem had not had a game in the same amount of time that earthbound did but that brings me to my second point. Earthbound had a game in development during smash 64's development. It was not irrelevant to nintendo at the time and sakurai revealed that if Earthbound 64 was not cancelled Lucas would have replaced Ness in melee. This last part is assumption but had earthbound 64 released prior to smash 64 it's entirely possible that we never got Ness and instead it was always Lucas.
Weren't Mewtwo, Snake, & The Ice Climbers unique?
There are reasons these guys were cut though. Ice climbers for technical reasons, Snake (while having no actual proof) was likely cut as he is not relevant to Nintendo and is a 3rd party which is an exception and mewtwo was going to be in brawl. He had an announcer call and everything. He was cut in order to make way for sonic who got added last minute and the inclusion of sonic was a higher priority than mewtwo.
History or not they were still pretty irrelevant by the time they were thrown in.
I understand they were irrelevant but like you said, sakurai likes surprises and those two are much bigger surprises than King. K. Rool would have been. A new franchise and a meaningful one