The question is what you really need feature-wise, and what money you want to spend. I guess if you got the HDx card used 1.5 years ago you most likely won´t have a current encryption code/software license for it. So you would (at least I would heavily recommend) upgrading to V12.5 anyway.
Then you need to get a new computer. The HDx boards will only work in all but the latest revision of PowerMac G5 systems (all G5 systems that had PCI-X slots; be aware that there was a “small” G5 configuration that had no PCI-X but older “regular” PCI-slots which are not compatible with the HDx board; plus the latest revision of G5s was moved to PCI Express, which is also incompatible with HDx). You most likely will be able to get a used PowerMac G5 on e.g. eBay cheaper than the current MacPros, but you will be at least 3 revisions behind the current CPU line (2nd (or even 3rd, depending on how you count it) revision of MacPros out there, plus the latest rev of G5 Macs which does not work with HDx). So while you will save some money there you will “only” get a system that has 2*2.5GHz max. While this sounds impressive and is quite fast for SD work, you will run into trouble if you e.g. want to work with HDV sources due to the CPU power needed for transcoding.
So while I think the HDx hardware is still an excellent solution and I would not see a urging need to upgrade a HDx system to Aja if you don´t need the extra CPU power e.g. for HDV support or a lot of rendering, I currently only would recommend getting a new G5 Mac if you really need to get this together cheap. Everything you put into this system (RAM, SATA- or SCSI-cards,…) is already older generation stuff and cannot be used anymore if you want to upgrade to an Intel Mac later. So if you have the money I would recommend getting the “smallest” (8*2.8GHz) MacPro with the standard graphics card, which is more than sufficient for most of Media 100s needs. And think about if you really need a Kona3 card, or if a LHe could be enough also. The LHe is missing some features (SD 4:3<->16:9 realtime cross conversion, HD 720<->1080 cross conversion, theoretical 2k and dual-link SDI support, SD to HD upconversion), but has some features the Kona3 card has not (HD/SD Component in, analog XLR audio out). So I guess for most users a LHe board is the more efficient choice.