There arent because I dont think they had them that early. They started manuals with Geneforge 1 and Avernum 3.
I wonder from what you get this, I still have the whole series installed on my HD with OSX 10.6.8, still able to run the old versions and I have the pdf manuals for 1&2. They are named Avernum 1 Instructions and Avernum 2 Instructions, but it's totally similar contents than Avernum 3 - Manual for example, including starting hints for example. It's 48 pages for the 1 and 58 pages for the 2.
It's almost certain those pdf manuals was not available at initial release, but they was still available later. Avernum 1&2 also provided the global map (the 3 has probably this map included in the game, not the 1&2) and this was most certainly included in CD release but they are quickdraw format, would be easy to convert them to pdf for example.
It's definitely files I would expect Gog includes, they are the reason I buy digital releases, particularly on Gog, to not have run after files and be sure have them back if I lost them. Well in case of Avernum 1 to 3, it's also to have a wrapper provided.
If this can help I can provide those files.
EDIT: As quoted in this thread a manual is provided inside the game Avernum 1, and it shares a lot of its contents with the game manual. But the pdf is much more handy, you can read the pdf before to start the game, it has a large party creation section, which is also available in game but still is handy to check through a manual.