The CWGC lists every casualty whose death was even remotely attributable to war service; this includes those who were killed in action, died of wounds, died of disease and those who died on active service. The example in question is not unusual; I have recently researched a casualty who died of cardiac disease dueing WW1 whilst serving with the marines. Although he was initially omitted from CWGC records, more recently his case was presented to them and he can now be found on the CWGC website.
The type of service number we are discussing was not introduced until 1885; prior to this date marines did have service numbers, but they were not unique and had to be used in conjunction with a company number. In fact the latter was more useful when identifying individuals, so it was more common to see individuals referred to as:
Private A.N. Other 14th Coy. RMLI
When the new numbers with a divisional prefix were introduced, all men currently serving were re-numbered. I've rechecked my notes and based on this number I'm fairly confident that he enlisted prior to 1885.
Rgds,
Alex.