I'm stumped. Both Castlevania and Metroid output at 512x480. That's really odd that the default CRT shader option plays nicely with one, but behaves differently for the other. @Lordmonkus I noticed you wrote a tutorial about using SweetFX / Reshade to introduce shaders last year. Do you see the same issue in both the standalone version with SweetFX / Reshade and the Retroarch version with integrated shaders? Aside from that, I may be out of ideas.
As far as audio goes, I just remembered that the Metroid game uses the jumping sound to indicate lava damage as well. I think it was a very odd choice for the developers of the Metroid game. But, they programmed the jumping sound to play in a rapid loop when the player is damaged by lava or acid. This means if you delete the jumping sound, there will be silence when damaged by lava (this may, or may not be okay for you). An alternate strategy you could try is duplicating the running sound and renaming one of them to the jumping sound (since they are the same sound anyway with the running sound just being a bit softer). I'm not sure if that would help.
In any case, if the popping sound is intermittent, and the Retroarch version causes it to occur more frequently, my best guess is that it may be a performance issue. I notice audio popping issues on my end as well if I have too many windows open while running Mesen. If I close the windows, it seems to get better.
With that said, programming of sound did require 6502 assembly knowledge as part of the replacement process. This was beyond my area of expertise. So, KYA (the developer of the Castlevania pack) was gracious enough to assist during this part of development with the Metroid pack. So, KYA may also know something of the sound popping issue that I may not.