We're making a lot of websites for multiple clients and we always had some problems figuring out what to do with "Updates". We're starting building Wordpress sites and there's almost a plugin update every week. Since our sites use WPML and Woocommerce, there's a lot of conflicts happening with unreliable WPML updates and other plugin with security flaws (revolution slider in my case).
I've just received an email from my client's hosting and he wants us to make updates from WP 3.8.1 to 4.0 but I know there's an intensive conflict job coming up. I usually use the 'Disable all wordpress updates' plugin to hide 'em all from the wp-admin.
I wish my project had enough budget to build custom sites, but that's not the case here.
I just want to know how Wordpress agency are with that. It doesn't look that professional to tell a client that updates aren't necessary.
First of all, you of course bill them for the time you spend on your clients websites. Better yet, sign some kind of support support agreement where they pay you a monthly fee for having their websites kept up to date and maybe uptime monitoring. You can also include a few hours per customer for support and small development tasks per every month(it's usually nice for the clients to have even if they don't use it every month). This is a nice way to get some steady income and fill the time gaps when you have less to do. You should also state in the agreement when you build the website that future updates and fixes is NOT included in price. You can give the clients a short period the report errors and bugs in the website and after that you will bill them for any extra time.
Secondly, get the right tools to optimize your time. I recommend ManageWP or InfiniteWP. ManageWP is slight better in my opinion and it is a hosted solution, but has a higher price if you have many clients(per client pricing model). InfiniteWP is a free self hosted solution(you set it up on your own server), where you only have to pay for the modules you use. You will need a few modules to get the functionality you need, but it's still much cheaper than ManageWP if you have many clients. For uptime monitoring I recommend Uptime robot(simple and free for up to 30 websites) or Pingdom a better service with a lot of nice tools, for example performance monitoring, but also a much steeper price.