Freeshop itself is a legal application when used with your own enctitlekeys.bin. It only becomes an illegal application when using encTitleKeys.bin from other users or that one site.Homebrew apps like Freeshop, that gives you free access to software and games is illegal. (It is considered as theft)
That in turn depends on the definition of "warranty": the commercial one, written in the manual, which is a private contract between owner and manufacturer (is void with softmods... unless you're smart and restore a backup);Keep in mind, modifying your system will break your warranty.
Since you bought it, it's now your property (the device) so you are free to do what you want with it. However modding it breaks Nintendo's Tos and they have right to deny any services that they provide to you (Nintendo E shop, 3ds repairs/replacements, playing on Nintendo game servers, etc)I've modded my 3DS but a friend said, this is illegal (mod without freeshop, etc.).
Is it illegal?