1 - No, it won't hurt, people are just THAT damn lazy that they want to bypass it.
2 - First go to the
AdvanScene database and search for a game (make sure to check "NDS"). In the results, find the entry you have. Make sure it actually has a number (that it's not XXXX), and the region is on the right-hand side, pay attention to that. Click on the game's name. In the new page under "Rom Info:" find "Crc32", that's the hash of the known-proper release.
Download
CRC32.exe and run it. Click the ellipses button (...) to the right of the file box and select your ROM file. It may take a minute to calculate, then it will display the CRC32, which you should compare to the one listed on AdvanScene. If you find that the ROM you're having trouble with doesn't match the known clean ROM, then you'll want to get a clean one.
Take note that a trimmed ROM
will show up as unclean, but in almost all cases a trimmed rom will work just fine (I trim all my ROMs with no issues). It's recommended to trim your ROMs if you want to save space, depending on the game it can trim off anywhere from 1-100 megs of space (it works by deleting blank padding data that's only in the ROM due to technical requirements of the original carts).
3 - Game saves go into the folder that the ROM is in. Don't worry, they don't show up on the ROM list in AKAIO.
4 - To remove a game yes, you can just stick the flash card into your computer and delete it. Alternately you can open the AKAIO start menu (press start or press the start button menu on the screen) and there's an option to delete it there.
5 - Yes, if you buy an 8GB card later just copy the contents of your first one off, then put them on the second.
6 - AP is "Anti-Piracy", it's coding put into games that can detect if it's running from a real cart or a flash cart, and if it detects it's running on a flash cart it will mess up the game in one way or another. This is why you make sure to stay on top of firmware updates (and why people using carts without firmware updates have to patch the games to remove the AP).
Most AP simply stops the game from loading, but other AP can simply try to annoy you to get you to buy the original (the AP for a Michael Jackson rhythm game blares a vuvuzela over the actual music, and the AP for the megaman zero collection screws up all the background graphics), or downright mean (the AP for the old SNES game Earthbound would wait until halfway through the final battle, then lock up and erase your save data).
Generally when people talk about "patching" a game, it's to remove the AP in order to get the game to run correctly on their outdated/abandoned flash cart.
The Acekard 2i is not outdated/abandoned, it's still getting proper firmware updates and game fixes, so the only time you would want to consider patching a game to remove AP is if the game comes out and you're too impatient to wait for an AKAIO update to fix it.