Exactly so. They represent an amount of bitcoins, which is not the same as representing actual bitcoins, in the same way that the number written on a check represents an amount of dollars, not a specific set of dollar bills.

It certainly isn't an obstacle so far as the bitcoin system is concerned. The bitcoins are just placeholders; it doesn't matter what they are, or even if they really exist. It does make a difference when trying to determine what we're actually trading--if anything--for legal purposes, however: commodities, currency, information, etc. Currency is particularly slippery. Outside of the bitcoin system, even fiat currencies which exist almost entirely in the form of digital records represent physical objects. We're expected to believe those computer records are equivalent to actual Federal Reserve Notes, even though there aren't really enough FRNs in existence to balance the accounts. It seems likely to me that if bitcoins can't be considered commodities, then they can't be treated as currency either, even if the bitcoin system as a whole amounts to a currency system.

The closest non-digital analogy for the bitcoin system seems to me to be a multiplayer game, where the bitcoins are the points. So far the legal system does not attempt to regulate gameplay, intervene in disputes over the rules, or tax people on their scores; hopefully this will remain the case in the future.