You are right. He does seem incapable of subterfuge. And his inclusion of his thoughts on Henrietta, reveal the turns of his mind that seems to meander along, quite without purpose or guile.

Perhaps its only my own heightened sense of anxiety on behalf of Anne, that "yes, by all means it's time to get Frederick to Bath already!" that I think everytime I read this chapter, that I am inclined to see this line as him fishing for some reaction from Anne that would tell him how to procede getting them together.

But it's probable that the Admiral is too scattered in his thoughts to really notice Anne's subtle reactions. We could easily imagine Anne's quiet blush and inability to answer his question and the Admiral being accosted a second later by another sea-faring friend that the whole moment would be lost. It is only because it ends the chapter, that it crystalizes in our mind this way.