by default it looks like options > preferred aspect ratio = 4:3 by default - https://github.com/libretro/snes9x/blob/master/libretro/libretro_core_options.h#L81, so you must have changed it at some point, yeah.
Yup, I just set up a clean RetroPie 4.7.1 card, and the defaults give full 4:3 for Snes.
Not for Megadrive though: for the lr_genesis_plus_gx default configuration the game image is not quite 4:3 - skinny black bars at left and right. The default config probably wants aspect_ratio_index=0 (for 4:3). Or a little overscan?
i wouldn't want to make assumptions. it could be true to the real hardware. you'd have to drill into the core options and/or the code, but since we use 'core provided' as our default, and generally use default core options, the default aspect ratio is at the discretion of the core developer, so it's typically intentional.