How does it work then on other lines that have a much later service each day of the week? SWML, GWML, BML, SEML, CML....
SWML: They actually cancelled (well, permanently bustituted) the 0105 on Sunday nights beyond Basingstoke for this very reason. But even then, the main line as far as Basingstoke is four track, and the 0105 has adequate slack in its schedule to allow for two of the adjacent tracks to be closed for engineering work (using special arrangements, mind you, as the signalling does not allow for this) if need be. All the two-track sections as far as Southampton also have bidirectional working so (though I don't know for sure) I'd imagine it's possible for one line to close late at night.
GWML: These seem to be sometimes partially bustituted (at intermediate stops) to allow for major diversions. But even without that, you've got the Sunday GWML service being atrocious so that they can close two of the tracks for most of Sunday. I imagine this rather makes up for it on the section towards London. On the sections further out I believe there is a reasonable amount of bidirectional working possible which would allow one line to close at late nights (correct me if I'm wrong).
BML: This line is pretty much designed with being able to carry out engineering work in mind. There are large sections where the traction current can be turned off to just one or two lines to allow them to be maintained while others are open. Further on there's bidirectional working on the two-track sections as far as Preston Park (from which trains can always run via a reversal at Hove if the line needs to be closed for engineering works; there's also running via a reversal at Lewes possible). However, you're right that this has been causing some issues, and I know many of the late-night services were cancelled in the medium term to allow a backlog of engineering works to be carried out. I imagine this line probably gets more weekend closures than most for this very reason as well — something that really doesn't want doing on the West Coast Main Line if it can be avoided.
SEML, CML: No idea, I don't do Southeastern much, but I imagine a similar story applies here.
Bear in mind that the WCML only really has one sensible route to Birmingham beyond Rugby — via Coventry and Birmingham International. This is double track and doesn't have the signalling arrangements in place to allow for regularly scheduled single-line working. You could argue that that could change; I don't know exactly how that would affect the last train times if it were. But beyond all that, these lines also must get hammered much less than the WCML. The WCML has 125mph tilting trains round sharp bends along with a lot of freight, and that can't exactly be healthy for the track, compared with 100mph commuter EMUs over relatively straight track. It wuold not surprise me at all if Rugby-Birmingham needs a lot more maintenance than Basingstoke-Southampton, Swindon-Bath or Three Bridges-Brighton.