Is there a reason to use extremely abbreviated table names? We're using a database setup from a vendor's application that has horrifically hard to read database table names, and no documentation on what is stored where. I can see why one might want to obfuscate their table structure in a proprietary app, but one of the selling points of this application (Enterprise Resource Planning) was it's customizability.

Table names are like aptrx (Accounts Payable Transactions) and apmaster_all (curiously, this is the vendors table). It's an extremely complex database, so I was wondering if there was any logic to the convention or if it was simply being obfuscated intentionally or otherwise.

To the best of my knowledge the length of the table name won't affect performance noticeably, correct? The database is very complex (hundreds of tables) so sorting makes sense, but I can't imagine why AccountsPayableTransactions isn't preferable to aptrx....
Oracle has had a long standing limit on table names of 30 characters.  I suspect this is a legacy issue based off an original 16 bit environment.
The length of a table name could have some minuscule effect on performance as all the names have to be stored in a data dictionary and also parsed for queries but I don't think you could measure the hit.  

A more important effect of short table names is that it's hard to work with.  I too have to maintain an enterprise database schema with short names.  There is no good reason to have short table names.  Ease of maintenance trumps obfuscation or old DOS habits every time.