Edit 2: Putt's back, the Canary has been updated, and I'm glad to have been wrong.
A gag order could stop Putt from removing the Canary (I think), but they can't compel speech by making Putt submit an updated Canary. So this long silence and lack of Canary updating would most likely be what we'd be looking out for to know if this site or one of its users were under investigation.
inb4 the usual suspects start calling me a shill and call my account activity into question; I'm not telling you you have to quit Voat or be mad at Putt. I'm just pointing out that the Canary is doing what it's there to do.
edit: And FWIW, Putt did make that one salty comment recently. If they can't force him to update the Canary they couldn't have forced him to write that.