Steven expands on his reason for not featuring Ward in the annotated chapter one (PDF): "Mycroft Ward doesn’t appear either. Mycroft is a very offstage villain, like Clio’s cancer. With a cancer, often you don’t get the relief or the release of a one-off face-to-face confrontation. To all intents and purposes, victory or defeat has to happen in the abstract."

Mycroft Ward's physical body died at the end of the nineteenth century (see pg.199), so that original version would not have been able to make an appearance in Raw Shark, and the closest Eric might come to encountering the online version would be to access it through a computer, which is what happens with the laptop.

However, I would argue that Eric does encounter Ward, through his proxy, Mr. Nobody. As Clio notes, "Nobody had been one of Mycroft Ward's most important operatives" (pg.253), connecting with the online database version of Ward.

While Clio points out that no one person could now contain Ward's massive online consciousness (pg.204), it does still manage the "various bodies online with standardising downloads and information-gathering uploads".

Mr. Nobody was just as much an echo of Ward as the other thousand or so individuals that participated in the "standardising process"; and Eric encountered Ward in the form of Mr. Nobody.

Nobody does say that he has to file reports on a regular basis (pg.134); if he participates in the upload process I don't see why he wouldn't participate in the "standardising process" as well.

There is also Nobody's "conference call" (pg.142-143) where he seemingly has a conversation with himself: "don't let him talk" and "we never know what he's going to say". Nobody describes this as: "Conference call. The office."

I assumed the "conference call" was Nobody's original personality breaking through and then arguing with the part of Ward that was within him. In light of Steven's comments about Mr. Nobody and Mr. No-one I suppose it's possible that it was Mr. No-one on the "conference call" though.

This doesn't preclude Ward's appearance in the novel; the laptop connection, in my opinion, is the closest Eric might have gotten to confronting Ward, save for encountering one or more participants of the "process".

In that case, what do you make of the dialogue between Eric and Nobody?

"You know I'm dead, don't you? You do know. All of it. Its obvious." -Nobody

On pg. 143 Eric sees a change creep over Nobody's face, it becomes serene and angelic , the way a face in a coffin becomes serene and angelic, calm and wise. Then he says "The important thing now is to give up. You know the truth. You know you're already dead. Deep down you know it. Eric Sanderson's gone, a long time gone. And Clio Aames. All of it, everything he was is over now. You should let his body go too... Storms on the surface can't hurt us anymore."
When Nobody's 'other' personality takes over for a brief moment he says "We're the same dead not-person." What does that mean? And his eyes that are devoid of communication, understanding and soul represent peace? (pg. 144)

So part of Mr. Nobody is Eric and part of Mr. Nobody is Ward?

.....Speaking of which:
Dr. Jekyll and Mr. Hyde
Je Kyll and Hyde
I Kill and Hide