I'm not overly familiar with the GE90 (haven't worked it for over 15 years), but filter bypass is indicated by a delta pressure measurement. On the older engines it was a switch that tripped at a preset delta P - newer engines use a transducer to measure the delta P and set the EICAS message when the delta P exceeds the preset level (I'm reasonably sure the GE90 falls into this category).
I don't know if the GE90 IDG would leak oil if the filter was missing, but assuming it doesn't there would be no indication. The delta P through the filter would be zero since there wasn't a filter so EICAS would be none the wiser.