If she keeps one bottle a day for another couple months, she'll be fine. I have a friend whose daughter kept a night time bottle until she was 15 or 16 months old.
On the fluid intake -- she's fine. She's not drinking much from the sippy cup because she prefers the bottle and she's holding out for it! She's not in danger of dehydration as long as she's drinking that morning and evening bottle. When she's fully switched over to sippy cups, she will drink more form them because it's her only option. Sure, she may hold out for longer than you think she should (toddlers can be insanely willful, as I'm sure you remember from your first child!), but she will eventually "get it" and drink from the cup.
As far as the crankiness, if she really was attached to the bottle, you'll draw out the "withdrawal" and possibly increase her anxiety about it by gradually reducing the number of bottles. Cold turkey is probably the best way in that case. Also, right around the 1 yr birthday, they're getting molars. Those things really hurt and they are slower to come in than the other teeth. This could be the cause of her crankiness rather than the bottle issue.