Is this something that will be fixed, or is this something we have to deal with?
I'm currently working on a fix for this issue to prevent anyone from being harmed by potentially malicious code.
The fix requires an update to the CPLD logic. It's the same procedure as updating CPLD logic of Ultimate 1MB, Incognito etc - you need a JTAG cable and Xilinx software, or send your cart back to Wolfram and he'll update it for you.
It also requires slight changes to the software, but that's no big deal (at least not for you :-). When the fix is ready just download the new The!Cart Studio version, export your workbook again, flash it and you are done.
I'll keep you posted about the progress, I hope I can release the fix soon.