The problem here seems to be that certain speakers just aren't very good, I'm not sure if there's a solution, since there's no way to check if the user has a set of $1,000 5.1 surround sound speakers plugged in, or is using headphones, or if they're using the generally crappy built in speakers on a laptop. This is actually a problem for pretty much anyone, since even if you could check their hardware configuration, the user might have their hardware configuration set up wrong, or they might occasionally switch out their 5.1 speaker system for a pair of crappy headphones because it's 1am and they don't want people calling the police for noise complaints (or they don't want to wake their roommates/parents/etc).
So, the best solution would be to make sure your sounds sound good on a decent pair of speakers, and they all have an equal volume between themselves. Basically, no sound is ear drum breakingly loud, or whisper quiet when compared to the other sounds. If your game has speech, then include subtitles so users can play with the sound turned low, or muted entirely. Include volume controls so users can set the volume themselves (including a mute button because that 30 second music loop is starting to get annoying).
In short, you can't control if someone has bad speakers, so don't worry too much about it. If sound is vital to your game, then include a note at the start saying so.
Sidenote: there's probably some fun stuff you can do in audio editing programs to fix some the issues with lower or higher pitched sounds, but all speakers have a maximum and minimum frequency range, and there's very little you can do to check that, even if you were making a native game (except for mobile development, where you know the range in advance)