Is the internal screen of the Thinkpad is deactivated when connecting 2 external screens?
Or might it be possible to work with 3 screens in total (1 internal and 2 external)?
Only with a separate video card in the dock.
I wonder if the graphic card of the T400s (onboard graphic) will be powerfull enough to drive 2 external TFTs, each at 1600x1200 pixel.
Yes. And much more than that. Far weaker video cards can accomplish that without sweating.
Will Windows still be able to switch between the settings automatically by remembering if the Thinkpad ist docked or not?
Sometimes it may, sometimes it may not. It is likely that it works some percentage of the time, but not 100%.
If not: how can I change the settings automatically by additional sofware (Ultramon?)?
Lenovo's Presentation Director (Fn+F7) allows you to switch to any scheme in just a few seconds.