I am not well-versed in the technical details behind bitcoins, but does the nature of bitcoins make them vastly easier to track than normal currency? E.g. if the attackers try to cash out or transfer the stolen bitcoins, is it much easier to flag them?
Not if you know what you're doing, no. Investigations of previous thefts have shown that you can't really hide bitcoins by shuffling them around. However there is a number of bitcoin addresses from services like exchanges that you can transfer bitcoins into and then out of to effectively launder money. An investigator would need the cooperation of the exchanges to track this money. The attacker will almost certainly move this money through a half dozen or more exchanges in equally many legal jurisdictions. Good luck following that trail.
Where the money goes is all publically available, yes. But it can be split up and fed through any number of accounts (you can make as many accounts as you like) to try to launder it. Also, does Silk Road care where the bitcoin being used to buy drugs came from?
I believe Silk Road is operated by actual agorist, or market anarchists to be more general. If that is true, even they would care about where the money comes from, especially if it is stolen money.