I played with the last patch (which included saving/loading) and completed the game 100% with no issues and used saves/loads often to test, all while using SNES9x-libretro's slowdown reduction/"overclock" option at "Max", but in the latest patch released today (NG+ included), the save/load feature hangs at a black screen if using the "max" slowdown reduction option, which otherwise has worked without issue for 3 full playthroughs of vanilla X3 as well as 2 full playthroughs of Zero Project prior to today's NG+ beta patch.
That said, I know the huge, ingrained belief that "overclocking will break everything" but there are games that can take advantage of this and X1-3 are prime examples where it works really well. If possible, it would be great for the latest patch to be altered to run with the "Max" slowdown reduction option. (For that matter, it could probably be fixed if libretro SNES9x just had exposed options for all 3 values it tweaks, but until the option is ported to standalone SNES9x, I wouldn't expect something that """in-depth.""") If I can help test a "fix" to this or something, I'd be more than happy to help however I can.