Should we infer she expects to recover from her wound

Yes

and signals gratitude?

and No

It seems clear that Ares fully expected to recover but the sign she makes is actually explained on screen as...

"Be Seeing You".

It seems more likely that this is to be interpreted as a threat rather than gratitude. It's more like "This isn't over!" than "Thanks for not killing me!". There's little to go on given the nature of the interaction but she hardly looks grateful...more resentful.

Should we infer she expects to recover from her wound

Perhaps not: at the end of part 1, Viggo Tarasov clearly knew that he had been fatally wounded by Wick. The last thing he said before dying was,"Be seeing you".

One explanation (which would tie in with themes around redemption in both movies) would be that this means "Be seeing you (in Hell)".

A slightly more left-field explanation is that Wick is already in a "Hell of eternal return". As (admittedly not conclusive) supporting evidence:

• It's possible that a couple of the distinctive henchmen (like the bald guy with the Rasputin beard) killed in Part 1 can also be seen again in Part 2. If so, then either the filmakers don't care much about continuity or else they're making some deeper point about Wick's world.
• Wick is travelling in something of a downward spiral with a definite pattern: every time he returns 'back to the start' (his home), his circumstances are worsened.