Are the SageMath app versions signed with an Apple Developer ID? If not, this strengthening of Gatekeeper may not be an issue for SageMath at all. Currently, there are three categories of Mac apps:
1) Those in the App Store, which must come from a registered Apple Developer and are reviewed by Apple before posting.
2) Those not from the App Store but that are signed by a Apple Dev ID.
3) Everything else. To run anything in this category, the user has to click various things saying it's OK to run "untrusted" code.
As I understand the link, Apple is increasing their oversight in category (2): not only must the app be signed but it must be run through some automated Apple website that searches for nefarious code and adds a signed cert confirming that. But that won't change anything about category (3).
Best,
Nathan