My advice would be to get them sewn, rather like little softballs. I don't think a latex coating would help, unless it was a really, really thick coating! Something like leatherette might make robust, but soft skulls.
Maybe some shops are stocking squishy toy skulls for Hallowe'en?
http://www.edirectory.co.uk/pf/880/mia/ ... id/5725225
They might be a bit big, but along the right lines.
Failing that, you could have 'actual' shrunken heads sewn. The mouths and eyes on genuine ones are usually sewn shut, I think. I must admit my expertise on the subject is a little rusty...
EDIT: Another thing worth looking for is erasers that are shaped like skulls. These ones are flat, sadly, but a hunt around your local shops might produce something a bit more like a ball:
http://www.jellyandicecreamparties.com/ ... raser.html
You could buy a few of those rubber glow-in-the-dark skeletons and use the skulls from them. You'd probably need to pad them out in some way.