Sure it was a bit dodgy then, but we're not in 2001 anymore. Patches these days generally don't have to be installed in a certain order and all that rubbish; most of the time you can just download one big one that overwrites anything before (keeping configurations, obviously).
I'm not really sure how using an example like Battlefield 1942 is really relevant. Even its successor, Battlefield 2142, has a handy news ticker at the bottom of all pages on the menu which notifies players of new patches. And the patch overwrites any previous ones, including the game as freshly installed from its DVD.
As long as players are properly notified of new patches and the developers have produced the patches properly so you don't need to go 1039 -> 1040 -> 1069 -> 1080 -> 2010 -> 2060 -> etc, it's no real issue.
Of course, I do find it bewildering when games don't take advantage of the ability to notify players on the menu of new patches. Tribes 2 cracked this one years ago by simply doing a check of Sierra's web servers when the game's started.
As far as I'm aware Source mods already have the ability to display web content in the GUI, so it shouldn't be that much of an issue to implement.