I think you've put your finger on a potential problem with running applications from the card. To access the card, the N800 (or N810) must power on the card, so frequent accesses will drain the battery faster. The kernel turns off power to the card when not in use, it's part of the power saving strategy of the omap platform. It can turn off various part off- and on-chip when not in use, and it can fiddle with the voltage levels too.

But it all depends on how often the card needs to be accessed. When cloning the operating system to a card we know what happens: An application is initially read from the card, page-by-page as needed, and after a while it'll all be in RAM (the part that is used, anyway) and there's no need to access the card merely because the program is active. But we don't know how GVM is handling the card when we launch a PalmOS application from a card. Someone could possibly trace this with 'strace', for example.

Then there's the question of storing data on the card. Do you have Agendus data on the card? Is it accessing it often?