Yes, Independent Analytics is fully compatible with multi-site installs.
You can Network Activate it to enable it for all sites on your network, and they will each have their own tracking and analytics dashboard.
Pro license activation
If you are using Independent Analytics Pro, you can Network Activate it just like the free version. Then, you can visit the Plugins menu, scroll to the Independent Analytics Pro, and click on the Activate License link. You’ll see a pop-up where you can enter your license key, and there is a box checked by default to activate the license for all sub-sites.

Please note that each subsite counts as a full website, so this will only be possible if your license key has enough activations for all sites in the network.
If you uncheck the box, you’ll have the option to choose which sub-sites you want to activate the license key on.

If you want to make a change to which sub-sites are activated in the future, you can visit the Network Admin > Independent Analytics > Account menu. You will find a Sites section there where you can activate/deactivate the license key on individual sub-sites.

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