One of my PCs saw showed me something today (thankfully he didn't actually want to do this). On the Prides table, Wealth gives the player an additional acquisition at +20. This particular entry has been discussed at length elsewhere. However, when a Heretek has this Pride and is combined with Mechanicus Assimilation (only Rare instead of Extremely Rare for Heretek), it is entirely possible for the PC to buy up to 100 Mechanicus Assimilation, therefore giving him 100 armor.

Again, thankfully this person did not want to do that because he thought it was stupid. However, I may end up GMing another group and I wonder how this particular situation could/should be handled. Thoughts?

Cap it at 5. Problem solved.

Larkin said:

why 5 instead of 10? is that extra 5 really that much when compared to space marine armor?

Well, with that Pride you can get a terminator armour out of the character creation as a space marine. So yeah, its quite a big of a thing that you should agree with the players/GM to what extent you can get stuff with it so that the game is fun for everyone.

Mechanicus Assimilation doesn't mean that you cannot wear armour. And AP from both sources stack. So as a heretek you can potentialy start with 13 AP (4 Mechanicus Assimilation, 7 light power armour, 2 armour-mongrel) - as much as termi armour and you can still run (and didn't even use wealth yet).

And my reasons it should be normally capped at 5 are caps in other systems and levels of machine trait in some enemies in comparison.

My take on it is this. In order to receive additional armor rating from having replaced so much flesh with machine and it ought to be a sizable chunk. I mean one bionic ear does not armor make. So I think 5 is reasonable number to represent the majority of the impure flesh to be stripped away and only the barest essential organic bits to sustain life.

I'd definitely impose a cap. Rules As Written is fine in most occasions, but the whole point of a GM is to moderate on things like this so that the game runs fairly and smoothly.
I'd cap it off at Machine (5)

A cap at five makes the most sense to me. To have enough of yourself replaced to provide the same protection as plate armour means there isn't much of you left to replace.

The other systems have a limit on the number of cybernetics a charater can have, but I forget if black crusade does as well. If it does, just use that as the limit, and filling that limit would prevent other cybernetics from being used.

No real limit in BC. Also seeing as many hereteks cn replace everything but some scraps of brain with cybernetics, such limit would have to be higher for them.
What is funny is that you can get mechanicus asimilation 5 which should turn you into preety much T-1000 and still bleed and heal yourself with medicae (and get cybernetic arms/legs/respiratory etc.) but I'm happy to abuse it.

Instead of treating it as an item acquisition, treat it as a service. Obtaining an implant isn't just getting the item, it's also obtaining the services of a technician/medicae to have it implanted. That way, you can't get it multiple times from a single roll. Then, considering that it gets more difficult to install as more and more of your body is replaced with unholy/blessed machine, increase the difficulty to obtain by one step for each level you already have. This way interested players have a gradually increasing machine trait over the course of their careers rather than one lucky roll giving them a block of 5 that never improves.

There's a lot of things that can be 'fixed' in this way just by treating them as services rather than items, without needing to impose artificial limits.