Are there any guarantees that at some point in time the method that Visual Guard .Net uses to "hook" into the application will not be altered by Microsoft by a security patch, thus suddenly disabling the application security?

Visual Guard .Net relies on Microsoft Proxy System (Marshall) to manage the communication between DotNet components. In case a Microsoft security patch blocks this low-level technology, not only Visual Guard .Net will stop working, but also all DotNet applications, which is quite unlikely. More generally, there is a very tight integration with the DotNet security framework (certified by Microsoft).