Roto-Hatch only affects how fast you hatch eggs. It shouldn’t have any interference on the shiny chance. Even with Masuda Method, the shiny chance is still around 1/683 (or 1/512 if you have the Shiny Charm), and sometimes the RNG will just hate you; I’ve had MM hunts go over 2000 before seeing a shiny. Just keep trying and persevere is really the best advice when it comes to shiny hunting.