It depends of the operating system you install.
Fairphone by default comes with a pretty standard Android version with Google Play serices, so it will be impacted.
If you either buy a Fairphone from Murena (with /e/ OS) or from Iode (with Iode OS) or if you buy a standard one and install a version of Android without Google Play Services (like /e/ os or Iode), then you can still use FDroid.
If you either buy a Fairphone from Murena (with /e/ OS) or from Iode (with Iode OS) or if you buy a standard one and install a version of Android without Google Play Services (like /e/ os or Iode), then you can still use FDroid.