Considering that SR2 was in the 2050s, IIRC, maybe they just hadn't figured out the method for cybernetically implanting Ghouls yet?
Although, I do wonder where the R&D money came from if they did have to figure it out... Now that makes for some interesting thinking.
To be honest, it's kind of something that's inevitable starting with the Cybertechnology source-book and how it introduces Cybermancy. From then on, it's become almost illogical to fall back into the "it just gets ejected out of their systems once the change has taken place" thing there.
So, although SRII doesn't directly contradict itself on that point, like many things existing within that edition (and, to be honest, many games that appeared in the nineties), it's something that's all up to the GM to make sense of and decide upon the ramifications.
Certainly, taking a cue from SR3 and SR4 seems to be the most sensible approach.
As for Cyber-puppies:
The section about Critters in 2nd ed. gives you the lowdown on the consequences of cybering-up critters (them's fun!). The Corporate Security Handbook also delves into the topic and how Corps use normal, cybernetic-augmented and awakened critters (or any variation thereof) to add to their security detail.
