I suspect that one of the biggest drivers of cost in F1 is that the rules are so restrictive as to make the "blinding flash of inspiration" all but impossible, so the teams are left spending defense-contract size budgets to find frog hairs of improvement.
There are also customer cars, and rather competitive ones at that, running in the WEC. I would hazard a guess that that would indicate that the costs are MUCH lower to run in the WEC.
I also am not sure how the public exposure of the two series compare.