From my experience, you should have no problem doing this as long as you don’t use it in something that requires a sustained write speed (e.g. camcorder.)
I do this with one of my 8GB SDHC cards. I’ve hacked my GPS a while back such that I can get into its Windows CE OS and store all sorts of stuff on the card, including WinCE applications, documents, etc. while travelling about. As I use the card in the GPS, it also means I don’t easily forget it like I often would with a pen drive.
The following gives an idea of how much I’ve on my SD card:
Despite all the files and folders, this card also works fine in both my digital cameras, which I’ve used on a few occasions when I forgot to put the main SD card back in my camera or when I ran out of space.
The only thing to be aware of is that flash cards tend to suffer from write “stuttering” when they contain a lot of files that are regularly added and deleted, which is where the write process intermittently pauses when writing. Generally this doesn’t cause a problem if using the card for reading (e.g. MP3 playback) or taking photos, however, it does cause problems if you try using it to take video clips with, where the camera or camcorder requres a sustained write speed. For example, if I try using this above card to take a video clip, my camera stops after a few seconds with an error saying that the card cannot keep up with the recording.
The best thing to do is give it a try.
If you have a camcorder or use your camera to take video clips, just be sure to keep a dedicated card for that.