If you're running a multisite installation you can still benefit from Drop Guard.
There are several possible setups in this case:
Create a separate Drop Guard project for each website in your multisite environment, enable Drop Guard module for each and provide a unique access key. You will be billed for each website separately, but you will get the best picture of the status of modules across your subsites and full control.
Choose the website with the largest number of modules enabled (or better yet - all modules used in other subsites), and create a single Drop Guard project for this website. The downside is that it's easy to miss a module or two so that Drop Guard will not be aware of them - a huge security risk.
Create a separate private "master" website where ALL modules used in subsites will be enabled and create a Drop Guard project for it. This way you will be sure Drop Guard cares about the whole codebase without exceptions. The downside is that this private website has to be maintained separately, which adds extra overhead.