I think it's not about how cron will handle this jobs, but how these jobs will load your server (whether you decide to run them in same time or in different service windows).
It should not be any reason for cron to stop running these jobs, only server load. Also you can reuse /etc/cron.d/ structure to hold separate personal cronjob file for every website, using name convention that similar to site name, so you can easily manage these jobs.
If you going to run them in same time - you may reach limit of open file descriptors.You can control such parameter through /etc/security/limits.conf, or use ulimit.