What most hosts do is host their WHMCS (and maybe their website) separately to their main server so clients can contact them during any possible downtime.
It's also recommended to host WHMCS separate to servers used for clients for security reasons.
I would say a large majority of people hosting on a single server at a reputable host experience maybe 40 minutes of downtime a year, usually much less.
As Localnode said, you want to keep your content separate. For instance, if you host WHMCS on a cPanel server which is also where you deploy your clients, you will run into a problem if the cPanel server goes down, since your ticket interface (WHMCS) will be down and unavailable so that you can not make an announcement during an outage. clients, if they are able to open a ticket or make use of live chat while there is an outage seem to be more forgiving of downtime. On the other hand, this requires additional costs, but the pro's outweigh the cons in this situation, from our experience. We recommend using a small VPS for WHMCS (generally requires additional ports open to communicate with external services that you do not want to allow open on the whole, as well as keeps your data separated.) Lastly, reverse dns is especially important for WHMCS, as you will want to be able to have your clients receive invoice emails, new order emails, and most panel providers make use of one shared ip for all clients. If one client ends up with malware and starts sending out mass emails, this shared ip will ultimately become blacklisted, and then all of your service e-mails will start bouncing. Hopefully that answers your question