We have been recommending $29 Apple 1394 Thunderbolt adapter for our 1394 products since Thunderbolt was released. However rest assured, the Apple 1394 Thunderbolt adapter will serve you well and since Thunderbolt will be around for a while, you shouldn't have anything to worry about.
As far as we can tell there are no plans to deprecate Core FW support in El Capitan, it works just the same as it does on Yosemite. Apple does not discuss future plans. This would not be to Apple's advantage to disable the pro audio and video editing industry by making such a move.
As for PreSonus developing options for the Ai console, we recently released AVB and Dante option cards, consider adding a feature request to the Live Sound Feature Request area for features you want to see added to the consoles.