48 kHz is considered "pro" sampling rate. The reason for 44.1 kHz on CD's is subject to debate. Some maintain that the sample rate was lowered so that Beethoven's 9th would fit on a single CD. Others claim that it was because that rate was compatible with video equipment.
IMO 44.1 kHz is insufficient for professional audio. Personally I would prefer 64 kHz. Whilst Nyquist theorem is all well and good most people don't understand the details and simply state "the sample rate must be twice the highest desired frequency". The problem with this is as you approach Nyquist the filter demands become extreme. The more extreme the filter demands the more taps are needed, the more precision is needed, the more latency is incurred, etc. A 64 kHz sample rate would give you a nice, smooth roll-off from 20 kHz to 32 kHz rather than the brick wall you get with 44.1 kHz.
There is no hardware advantage to using 48 vs. 44.1. The costs would be the same in either case. Modern converters use over-sampling techniques to implement the necessary anti-aliasing filters thereby reducing off-chip filtering to simple circuits.
MP3s have no native sample rate but are typically 44.1 kHz because they are usually derived from CDs. MP3 is a psycho-acoustic compression format that exploits frequency masking to lower the data required to store audio information.