This does not sound like a failing hard drive to me.
Static only when using IP trunks would almost certainly be related to network connectivity problems (either bandwidth issues or some other network issues).
Loud static noise when making intercom calls on digital phones could be either an incorrect companding law selected for the phone(s) (ulaw instead of alaw or vice versa) or data corruption on the B channel (not very likely). The system could select an incorrect law if it mis-detects the phone type (e.g., NA vs. global set). Corrupt B channel data could be due to noise introduced on the connection of the MBM (DSM16 or DSM32). Both problems could be caused by a DSM module or its cable. If the digital phones that have this problem are connected to a DSM module, consider replacing the cable that connects the module to the BCM50 (you would need a shielded cable of the correct length) or replacing the DSM module itself (which could be partially failing). A quick test that you could do - move the phones to digital ports on the BCM50 and test if the issue goes away.