Application control is free to use without a license. It's the database updates that you have to pay for. In FortiOS version 5.4 this was covered under the IPS subscription, but with 5.6 and 6.0 moving forward, application control updates come part of the standard FortiCare support contract so you don't need the IPS license anymore (only support).
This is the reason it doesn't give you a warning when you enable it without licenses (the same with IPS and AntiVirus). It will still work but without the latest signatures.
This is different from the Webfiltering service. You MUST have a valid license to use webfilter, and if you don't have a license and apply it to your policies then your internet traffic will be blocked by default. This is why you get a warning saying that there is no subscription when you configure webfiltering.