[AgentZero]

E-research's unpleasant side-effects should occur before the research project is complete. ie: No 'Sire, we have developed a new WMG' that ends up exploding when you use it in combat. Research in SE should encompass both the research and development.
Possible side-effects of e-research might be a chance the project will be reset to zero & you'll have to start over (Ooops, we blew up the lab) and the results of you research becoming available to other empires ('Did I post the results of the Phased-Poleron tests on the secure R&D forum, or on the SEMXVI forum?'

E-intel would also have a higher chance to fail, since your skilled agents would be run ragged and/or you'd be fielding agents who weren't ready for covert ops....