Not a discussion of anything on a macro-scale, just small details that struck me as off. Feel free to add your own observations.

• Seems strange that Sages are better at Commerce than Desperadoes, when I'd assume "Underworld Fixer" would be one of the main types of Desperado. Sages get Commerce at 100*rank, Desperadoes get it at 150*rank.
• Given that First Aid is based on Agility, it seems unfortunate that Agility is so expensive for Chirurgeons to advance. Sages, who get cheap Medicae and Agility advances, seem to compete too well with Chirurgeons as medics (though obviously, Sages can't get Chirurgeon's AP-improvement for Medicae)
• It seems odd that Assassins get Investigate at 100*rank, but have pay 150*rank for Athletics.

I guess the desperado is more of "some shady deals in a back alley, still prepared to shoot you in the face if things go south" type of dealer, whereas the sage represents the wholesale manager of the spectrum. So if you'd want to play an Underworld fixer, maybe Outcast Sage would fit the bill better if you really want to specialise in commerce.

I agree with the high agility cost, that doesn't really make sense, especially coupled with the fact the chirurgeon's special ability specifically applies to first aid.

Athletics is more of a brute force skill, which entails lifting heavy stuff, running for long distances and that kind of stuff, all of which I wouldn't necessarily associate with graceful, lithe assassins. Investigate really doesn't make that much sense, although I suppose it might be used for finding out where your target is in the first place...I guess they just wanted to give another role other than seeker cheap investigate advances, seeing as it seems to be more important in DH2 than in the first version...

Investigate on an assassin makes perfect sense to me. As you said, they have to find where their target is in the first place.

To me, Investigate on a modern day assassin makes sense. On a death cult assassin, a little less so. But it's such a minor point, that I can accept if the writers have a slightly different vision of how a 40k assassin operates, than I do.

It provides flexibility. YOu can create a blade wielding murderer (Death cult Assassin), or something more subtle. As long as they allow you the ability to create both, I don't see either as being outside the assassin archetype.

Investigate is fine, it's the moving people around bit that makes me wonder why anyone would play an assassin.