Most modern emulation software (RetroArch, SNES9x) ignores the header and runs .smc files without issue. However, FPGA hardware (such as the Analogue Super Nt or the MiSTer FPGA platform) and high-end flashcarts (like the TerraONION cart hinted at by the search term) often require the ROM to be "headerless" ( .sfc ) to calculate the correct memory mapping (SDRAM). If you load a headered .smc file onto an FPGA, the game may fail to boot or display graphical glitches because the memory addresses are shifted by those extra 512 bytes.
If you want, I can:
Frontend tools like OpenEmu or Skyscraper0;545; use file hashes (like MD5 or SHA-1) to identify games and fetch box art. Headers change the file's hash, preventing a match. smc to sfc converter top