There are plenty of ways to destroy it physically (throw it in a forge, bend it with pliers, etc).
I'm a bit more concerned that a scammer wouldn't destroy the coin per se, but make a claim on authenticity, causing me to lose my money and also the coin.
1) Get the original (say, $3000 coin) carefully out of the holder - then smash the holder with a hammer.
2) Find a replica of that year coin, which really is a fake, for $10-$50. Scratch it up, bend it, whatever.
3) Send the original coin back for grading to be certified with a new graded coin holder and serial number, to be sold for $3000.
This is just the "kill them all and let God sort them out" mentality applied to property.
So to answer your question: In some cases, not well enough. ;)
EDIT: source: http://www.schneier.com/blog/archives/2011/04/euro_coin_recy...
Funny fact: at that time it was illegal in my country (France). This law has been abrogated since then to allow machines that crush coins to make souvenirs.