So, this is an old thread, but since the annoyance is still there, here's how you can fix it:
1. Go to your Stars in Shadow install folder.
2. Go to the "Lua state" subfolder.
3. Find the "startup_splash.png" file.
4. You can make a backup copy of it if you want (something like "backup_splash.png") just in case.
5. Edit it with a good image editor (paint.net or GIMP would do). Make the image entirely 100% transparent. You can do that by selecting everything (ctrl-A) then deleting it (del).
6. Save. Now the startup splash is invisible.
So when you start the game, you will no longer see it overlayed on your screen, blocking your web browser or whatever else you're doing while the game takes its sweet time loading.
Do not simply delete the file, this will most likely cause an error upon startup.