Hi testingNoobie,
Please do not hesitate to ask whatever interests you.
1) To be more precise, MCS is in idle and waiting for you to attach some USB removable drive and also triggers itself to all possible & known vectors attack that malware can exploit. avast! also monitors the USB device if it is set up in the settings.
The difference between AntiVirus and AntiMalware (MCS) programs is that AV scans are mainly signature based detection. MCS does not need to know is the file malware or not. MCS 'reads them', it reads the file and their executive behavior ...
To read more abaut signature & heuristic detection, you may read what I wrote here some time ago:
http://www.bleepingcomputer.com/forums/t/523938/mcshield-malware-remover-not-mcafee-is-it-safe/?p=32999852) USB worms based on autorun.inf file (autorun on XP's and autoplay on newer OS's) are not so common. This is one of the oldest known vectors attack and all AV programs does monitor autorun.inf file and corresponding file (again, only if AV know that file as malware). The ugly truth is different, today malware uses other vectors in order to bypass AV's detection and load itself in host system.
3) MCShield is an active (preventive) anti-malware program designed to prevent infections transmitted through removable drives.
Although I have not seen the actually USB mem-device with a real thousand files, but yes, scanning time may take a while in this case. But in most cases, MCS will verify the files in short. In this example, speed time may depends on disk (HDD) speed and actually speed of USB drive (removable drive) itself.