cia files are, by nature, archives. The file extension stands for "CTR Installable Archive". Most games are slighly larger when unpacked and installed than they are in .cia format waiting to be installed.
Reinand itself cannot run out of region cias by default. However you can do so by installing a program called "FreeMultiPatcher" and running it after booting emunand. You will need to rerun this program every time you reboot your system. One thing to keep in mind, updates and DLC will only work if they are from the same region as the game itself.
To swap your sd card to a larger one, the easiest way is to use a program like EaseUS or MiniTool Partition Wizard to clone the old SD card to the new one. You would then need to the same tool to extend the data partition on the new card to make use of the rest of the space.
Alternatively, you can use emunand9 or GW's menu to set up an emunand partition on the new sd card, then use emuNANDTool on your pc to extract your emunand partition from the old sd card, and then inject it into the new card. Once you do that you can then simply copy the entire contents of the old sd card to the new one, then place the new card in your n3DS.