I'm in the process now of converting discs bit by bit to FLAC. I'm using EAC and it has been a fairly easy process. I ripped about 5 discs and played around with a standardized naming scheme which i prefer.
I can't say i've seen much for cover art and whether the lack thereof has been or would be an issue, but if i had the option, i would like to have the proper cover.

"Those who preach the myths of audio are ignorant of truth."