Devilspie didn't work in my system for some reason. Eventually, I found a substitute (not so elegant).I installed
sudo apt-get install wmctrl
wmctrl -l found the names of the windows, I wanted to close on startup. After that, put those command into script (create new empty file and name it
.<...>.sh. Dot at the beginning of the name to hide it):
wmctrl -c <Window_1>
wmctrl -c <Window_2>
wmctrl -c <Window_3>
Finally, added this file to the startup applications couple of seconds after the targets.
Note, that this command closes windows. To start program minimized, on different workspace ets, find appropriate options in the program manual.