Yep, I have. It tends to slow down play as the DM spends time fiddling with objects to make them look correct for tokens that are visible and not visible - and then a player inevitably says - there's an enemy over there! - because the DM has left a canopy off because there's an enemy token under the tree. It's more hassle than it's worth.

I thought about doing semi-transparent canopies for a while, though that still looks a little odd with the tokens on top of them. What maptools really needs is layers...