The string action on an acoustic can be altered by changing the height of the saddle. Most of the time, this means taking a little off the bottom to lower the action and improve playability.
There's a danger in going too far though. Occasionally, a guitar's neck angle won't allow a comfortable playing action without making the saddle really low. More common is an older guitar that's been settling and shifting under string-tension for years. The saddle on these instrument may have been lowered again and again as the guitar reaches the point where a neck reset is needed.
Either way, you don't want your saddle too low. As the saddle gets lower, the angle that the strings 'break' over it reduces. Too small an angle and the transfer of a string's energy into the soundboard suffers.
This is even more of a problem if you have an under-saddle transducer (UST) pickup. These pickups use piezo crystals that depend on pressure to produce a good signal. As the angle drops, and you start to lose that pressure, one or more strings may begin to lose output.
What's the answer?
If it's necessary to have a saddle this low in order to achieve a comfortable action, it's probably time for a neck reset. Of course, that's not an inexpensive job. It can be possible to improve things by 'ramping' the string slots from the end-pin holes to increase that string break-angle. If someone suggests shaving the top of the bridge (the wooden bit the saddle sits in), you'll want to think very carefully about this. That's not something you really want to do on a nice guitar and it will devalue an instrument. It might be ok to get you out of a hole on something you don't mind getting beat-up, but it's not the ideal way forward in most circumstances (i.e. if your guitar is worth more than a hundred bucks or so).
it's worth mentioning that a low output from some strings with a UST/piezo pickup may not be related to this saddle break-angle thing. There are other things that can play into output and string-to-string volume balance issues. That's a discussion for another day, though.