I purchased my LS V8 with 75K miles and almost immediately started having coil problems. Put all new coils on the vehicle, (non-Motorcraft & non-Ebay), along with a plug change... and am now at 205K+ with no coil failures. I did do a coil boot change at roughly 180K when I did VCG's.
I do think that the covers trap heat from the cylinder head below, rather than letting it escape into ambient air. However,,, there is also another issue that will cause coil problems. There is a bulletin through Ford, about the wiper cowl seal failing, which allows water to dump onto the main coil harness going under the cover. The water migrates through the harness and causes coils to drop.
The only issue I have had with the covers off... was driving in a pouring rain on a section of road that didn't normally have standing water. When I hit the water, it was enough to drench the engine. The coils started mis firing, but dried off after a minute or two, (due to the engine heat boiling it off).
I'm not disputing anything else said here. Just offering my experience.
If someone has a VOM with a temp probe option, it wouldn't be too hard to check temps with one cover on, and one off. I'd do it but I'm so busy I'm lucky to keep up on oil changes at this point.