Mahogany guitars with glued-in necks tend to bring out bass frequencies, hence "dark".
In most Les Pauls, the thick maple top adds some brightness which balances out the darker tone of the mahogany (which isn't to say that you won't find dark sounding Les Pauls, wood is an inconsistent material and all guitars sound different!)
You'd have to compare your LP with other, similar, guitars to decide if it's actually dark sounding.
As for pickups, most humbuckers work well in a Les Paul. What kind of sound(s) are you after?