I have a 1998 E320 (v-6) with the same symptoms; 3-4 knocks at start up, hoy or cold. Mine did not occur when the a/c was OFF.
My brother-in-law is a MBZ mechanic and diagnosed it as the a/c compressor clutch. He said they all do this right after start-up to "check" the condition of the compressor (in case they're locked up) to prevent further damage.
So, have yours properly diagnosed first to rule out anything serious. Mine is simply annoying for now, When it completely fails I'll get it changed.