Can the bg1 expansion be loaded halfway through a game without any detrimental effects?

yes there will be no side-affects becoz it rewrites the files and completly changes them, it doesnt just add new ones.

As far as I remember, you cannot go to the new areas until you manually update your map by running a file in your BG folder.
Or was that something else?

It just overwrites some files which add the new game data to your original saves. The conversion is automatic and painless, unless your loading a "Final" save i.e. where you've completed the BG section of the game. In which case, you can go to the new areas when you want, but you'll have the final battle to fight, that's all.

"Can the bg1 expansion be loaded halfway through a game without any detrimental effects?"

I did it and nothing detrimental happened.

You are correct. Ulgoth's Beard and Durlag's Tower will not show up on your map (and you can't travel to a place that isn't on your map) unless you run the program called MCONVERT, which is in your BG directory. This is only necessary for games that were started before you installed ToSC: Games that were begun after installing the expansion will automatically have the updated map.