It's not that hard to find them, although many retail outlets definitely are not restocking 40GB SKUs on a regular basis for the simple fact that production has stopped, making availability limited.
I haven't seen a 40GB in stores for weeks.
MGS4 bundles are currently the only in production SKU readily available, and even that seems a bit sporadic since it looks like the bundle may well be a fairly limited production run, meaning it may cease production once the 80GB Core SKU rolls out.
I saw about two total during the debut month of MGS4 (when they were fairly scarce and 40GB SKUs were everywhere), and I recently saw a shelf full of the bundles (8 consoles) at a Fry's, but no 40GB SKUs. It seems the 80GB bundles are the only regular stock currently available.
Amazon is out of MGS4 bundles until the 20th, after being at the top of their video game hardware list for about two weeks.
If the MGS4 bundle stays in production, I'm not sure what the allure of the SKU would be other than BC, which matters mainly to core gamers rather than the average consumer that wants to play PS3 games. Most consumers aren't going to pay $100 more for a PS3 (than an 80GB Core) for a $60 game.
If it stays in production through 2008, it wouldn't surprise me to see a reduction to $450 for the bundle until production ends (or a much less likely upgrade to 120GB storage). If not, we'll be seeing less and less of the bundles being produced once the 80GB Core becomes available.