If your only requirement is to send notifications on the active workflows, and to do so every few days, I would think about doing so with a job running a report and not by workflow loops, since every workflow loop writes a lot of data to the database (step log, node log, container, links to object etc) especially if there are a lot of process of this type in the system.
This will also give you the option to send a list of notifications and not send them one by one, users who receive a lot of messages from the system tend to send them to the spam folder after a short time...