First I have to say that I played nearly all space sims, from Star/Free Lancer, Wing Commander, Freespace, X-Wings, Tie Fighters,.., but
I-War is my all time favorite!!

Now I have two version of the game, the first German retail (3 Disks) and the Deluxe Edition (4 Disks).
How can I get rid of the CDs? There is this -disk option, but how can I use this?
Just copy all to the given directories in the game dir and overwrite existing files?

How is that handled in the GOG version?

I recently did this myself, how easy it is depends on your operating system. XP or earlier should allow you to install fine, windows 7 and 8 64-bit don't support the 16-bit installer (not sure about the Vista or the 32-bit versions though). Here's what I needed to do to get it working under Windows 8 Pro 64-bit.

1) Installed the deluxe edition of the game on an old XP machine (both I-War and Defiance).
2) Zipped up the Particle Systems folder and the HKEY_LOCAL_MACHINE\SOFTWARE\Particle Systems branch of the registry.
3) Unzipped the game into the C:\Program Files (x86)\Particle Systems folder on the Win 8 machine, added the registry keys.
4) Copied the video and audio from the CDs into the \psg\resource\video and \psg\resource\audio_l folders
5) Installed nGlide and set it to 1920x1080, 4:3 ratio.
6) Created a shortcut to the game:
"C:\Program Files (x86)\Particle Systems\Independence War\IWar.exe" -b -16 -800x600 -disk
7) Edit the dreadnaught.ini file in the game folder (I may have tried running the game first to create it). Add the following lines:
VIDEODIR "C:\Program Files (x86)\Particle Systems\Independence War\psg\resource\video"
DIALOGUEDIR "C:\Program Files (x86)\Particle Systems\Independence War\psg\resource\audio_l"