This is very true - sadly.
The top nav of the NYTimes is a political minefield ("HOME PAGE, TODAY'S PAPER, VIDEO, MOST POPULAR, TIMES TOPICS". Part of the problem is that links to some of these pages exist nowhere else (or relatively few other obvious parts). Its a big big web site and over time some organization was lost as new pages crept in.
BUT... Do you know what happens if you remove it? Nothing. No meaningful impact on traffic. Yet there it still ives.
The Left Navigation bar on the Homepage is a recognized problem internally. However you need to weight:
- Same argument as above, some links to these pages don't really exist anywhere else (Skimmer, Times Wire, Multimedia, Times Machine). You need to solve that problem first.
- Various departments would make a stink if they did not have the glorious link from the Homepage.
- If you remove it, you're probably talking about a solution that would take up more horizontal space and push the content down even further.
Those are the two immediate ones that I recall. I don't see this being addressed specifically anytime soon - it was hard enough to clear space for the Facebook module.