I think the API should return the is_deleted! Having said so, if you want to make sure you have the latest version of the activity you could also use the is_current_revision=1
?
Editing to add a suggestion in the comments also by @ErikH, which was the solution I went for:
Not sure this is of any help but there is an extension for the CaseActivity API: civicrm.org/extensions/caseactivity-api