They would still be funding it. So if resources were impacted enough, they may not have wanted to spend on those. Most likely, the pandemic caused a big enough delay to BotW2 that they are holding off on any Switch ports/remasters to fill in any void in case it's a holiday 2022 or 2023 release.
Pikmin 3 was ready to go months before it was released, and was held back for that reason. It just amazes me that so many people act as if we weren't in a global pandemic(still are), for a year that seriously disrupted everything on the planet.
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Prime games are their own thing. They are like an AU time line. They have the same/similar themes but are not officially on the main Metroid timeline. That way Prime games can do their own thing and 2D can do theirs.