First point, LFE is low frequency effects occasionally present in the .1 channel in movies. Music has no LFE. With the notable exception of pipe organ music there's almost no bass content below about 40Hz.
Bass frequencies require no more power for a given level than any other; e.g., 20Hz, 200Hz and 2000Hz at 80dB use the same power. What is different is that deep bass frequencies are less audible to humans than are higher frequencies at the same dB level. If you want to make them more audible(or at least equally audible)in relation to the rest of the music, the simplest move is to turn up the bass tone control. There are also built-in or separate parametric equalizers to try to do this a bit more precisely. This boosted audibility of the lowest bass isn't "natural", of course.
So no, your system isn't "holding up the lower frequencies" and you aren't "missing something" that you're supposed to hear.
