I would start with the current version and try to get certified. If you keep waiting there will always be a new version in the wings. In the real world there is less concern about this issue. None of the current jobs I've been on have ever questioned what version of NT I'm certified in. 3.11 workstations along with NT 4.0 Workstation, Server and Windows 95 clients.
Many people are familiar with the demand for CNEs a few years ago and the certification glut.
Many of these folks are unable to find good paying work or are retraining in Microsoft. It is important to point out that the CNE's that saw this coming and got their MCSEs are in great demand due to the number of mixed environments out in the real world. Microsoft Solution Provider companies must have two MCPs on staff to retain their status and get job referrals from Microsoft. They need an MCSE or several MCSEs to get any large jobs referred by Microsoft. What I would recommend is that you keep your eye on the market closely and be prepared to switch teams if you see a trend developing.