The R4 card itself will not physically "break" your DS/DSi/3DS. It fits the slot electrically and mechanically. However, **using one carries risks** that can lead to a non-functional console.
ntrboot (for 3DS CFW) blows a **one-time eFuse** on the 3DS motherboard. This **permanently prevents** downgrading below 11.15.0 / official repair. It does not break normal function.**Softmod your 3DS/2DS** (3ds.hacks.guide). Free, no hardware needed, runs DS/3DS/GBA/GB/NES/SNES/etc. via TWiLight Menu++ + RetroArch. Safest, most compatible, supports cheats, saves, sleep mode.