I took another look at your setup. It appears that the Mini blocks the entire front vents on the SE as well as most of the inflow from the bottom vents. In theory the bottom vents are the most important vents allowing cooler air from the bottom to flow across the warm logicboard and up toward the heated air inside the case and out the top, particularly where pure convection is concerned. The SE is no more hermetic than the Plus was, except of course for the upper half where heat is surely trapped by the lack of vents. The front/back ventilation (without drives in place) would be far superior to the Plus.
If anything I would expect the SE to actually run cooler than the Plus, because of more efficient electronics. The Mini by comparison is a much hotter CPU. In fact I would argue it generates more heat than the SE logic and analogue boards combined, plus you have an LCD power supply in there as well. I know my MacBook gets unbearably hot on my lap in only a few minutes, compared to my PowerBook 100 which never even felt warm after running for hours. WIth a stripped down SE the main issue is the trapped heat at the top and how quickly that heat can exhaust from the rather large rear vent. If the PSU & logic board are generating most of the heat, I would expect natural convection to allow most of that heat to exit the back, or at least heat generated from those components. The analogue board is essentially in the same configuration for both Macs, so the main issue remains: how quickly will hot air trapped at the top circulate and evacuate, and how fast will that continuous heat take to overcome the SE's natural convective abilities to keep the temperature within rated tolerances. I would love to get my hands on one of those clear SE's to do a smoke test and see the convective airflow ...
Nevertheless, I think we all agree with your conclusion: don't run an SE without a fan!
Some thoughts on your mini, though. If the fan runs often, I would be concerned about the operating environment, especially if the SE is trapping most of that hot air inside the case. Essentially you are operating the mini in an environment that may be outside the mini's rated specs, despite the fan working to cool it. It actually makes me wonder if you shouldn't be running a fan in your SE too!