Odd, there is no limit for free users with cloudflare, though you get better tools for a higher price.
When you are under attack, you can do a 'Under attack mode' by toggling this on the main page for mangadex.org. It will give a challange for visitors. Bit annoying but you can look if It can mitigate a bit of the problems.
A challange for now is acceptable, but this load time isn't