1. No. Should work find on normal flash carts as long as you have not messed with the download play component.
2. Sure. It will tend to be a file called utility.bin, possibly located in a folder called dwc, or maybe something with nef files. Either way it will be a DS binary within the DS ROM (have its own icon and everything). There is seldom much point removing them as they usually all of about 4 megabytes, if not less (they have to fit in one go, run and have memory and guess how much memory the DS has?). Removing it as an option from the menu or something is a bigger ask as you will have to either fiddle with the menu to either loop it back around, put in a dummy file that exits or outright remove the option from the menu + any attendant graphics mods you care to do.
3. I don't follow, though if it is about cloneboot specifics you will have to wait for someone else.