If you normally install through application manager then the apt-get clean is done automatically for you. I think the problematic cases are when you point your browser to a .deb and click it, one option is to 'install', if you do then it will download it to /tmp/ and tell the application manager to install from there. That can be a problem if /tmp gets full. (If you instead saves to file, then later install, you bypass that problem). I don't believe it's normal to run out of actual application space in the flash file system, most uses for booting off SD cards is to get more choice (e.g. KDE, or dual boot etc.)