In PhabricatorApplicationDatasource, do a PhabricatorApplication::isClassInstalledForViewer(...) test on each application and skip it if it is not installed. You can get the class name with get_class($application_object).

In most other typeaheads we still return these results, but with "Disabled" or "Closed" or similar, which sorts them to the bottom of the list and greys them out. This makes it less confusing when a user types a result that they know should find a hit (like the username of a disabled user) and get nothing back, and is occasionally useful (e.g., to find tasks still assigned to someone who left the company).

In the case of applications, I think this is probably so rare that it's not worth bothering with for now.