It'll be years before AGP cards are completely phased out. I wouldn't be too concerned.
Plus, as long as it runs on the hardware you have now, does it really matter what it'll run on in the future? You're not using a PC from the future to power your emulation.
I guess it might be a problem 2 or 3 years from now if you want to build a whole new machine and pull the ArcadeVGA from the one you already have. Other than that, there's really no need for concern. In a couple of years, that card will have alot bigger problems than just being AGP. It'll be ancient in just about every single way.
If you think you won't be seeing new AGP boards anymore by the end of this year, you've fallen for hype. Hardware companies always push the "latest and greatest" because it showcases their abilities. However, you can still but a brand new PCI video card if you really want to. You can pop it into your machine and it'll work.