First of all, from one generation to another, the connector(s) used for the internal USB 2.0 ports have changed. You thus have to be careful which you order...
GORITE produces and Micro SATA Cables sells cables for almost all of the NUCs (see here for a complete list). The one you want for the WY NUCs is here. It is also available through Amazon here. International shipping may be an issue; you will have to check.
Modifying the case is simple if you have the WYKH version; there is enough room on the back panel to drill a ~3/8" hole to feed the cable through (I did this on a RYH unit). For the WYK version, this isn't as simple; the case does not have enough room for this hole. In the SY NUCs, which have separate connectors (and cables) for the two USB 2.0 ports, the cable connector was small enough that I simply fed it through the Kensington lock hole (on the side of the NUC). In the WY case, you would have to either enlarge this lock hole to fit the connector through or (something only possible with the cable for the WY NUCs) pop the pins out of the connector shell, feed the cable through the lock hole and then reinsert the pins back into the connector shell (if you do this, remember the pin order!).
If the path you choose involves drilling, filing or cutting the chassis, I strongly recommend that (a) you remove the board from the chassis while you are doing so, (b) you remove both the top and bottom covers (so they don't catch metal filings), (c) make sure that you round all edges (so they don't cut the cable) and (d) you thoroughly clean the chassis of metal filings before reinstalling the board and covers.
Using the extender cable is a good idea. Using a cheap USB audio adapter (my idea) works just as well (leave the connectors from the headset plugged into it all the time and just pull the audio unit from the USB connector when not needed). Insofar as quality is concerned, I can't tell the difference between the internal audio solution and the cheap USB adapters, but my ears are almost 60 years old and were abused royally in my younger days...
Another solution is to use an external USB 2.0 or USB 3.0 hub.
Hardware revisions are not usually documented externally (I couldn't find anything). The BIOS revisions are all documented here.
Let me know if I can help you further...
Oops, missed a question. No, the internal ports will already be enumerated and devices plugged in will be immediately recognized when they are plugged in.