I have my Pi 4 (which is great), but I also have an older Pi 3B+ where the microSD became corrupted and I finally got around to putting in a fresh one. I grabbed the download from the retropie website, put it on a new card, etc. But, I noticed two things: 1) that mupen64plus (not lr-mupen64plus, and not lr-mupen64plus-next which wasn't installed by default) is the default for N64; and 2) that updates were available for mupen64plus. The stock build seems to have mupen64plus current as of Oct 2020, if I recall correctly. Normally I would update a package reflexively, but I also remember concerns about regressions with an N64 update from around last year. So, my questions, specifically for a Pi 3B+:Should mupen64plus stay as default?
yes. standalone is fastest and most compatible. lr-mupen64plus (NOT -next) or mupen64plus-gles2n64 or even lr-mupen64plus-parallel may be faster in some scenarios, but the best balance is mupen64plus-auto (which i believe is the default for pi3), which selects the appropriate video plugin for mupen64plus-standalone, per game.
Is there any potential downside to installing the latest updates (since the most recent stock install) to these emulators on a 3B+?
not that i'm aware of, but as always, always back up before any updates. do note that n64 emulation is probably only going to get slower with updates, as emulation gets more accurate, compatible, etc.