I apologize if this counts as a necro, but eh.
Disclaimer: Not a parent, nor am I a professional in psychology or anything of the sort. Just giving my own opinion. I also haven't played through all the routes, so I'll be discussing individual issues rather than the characters themselves mostly, aside from Hanako, who I finished. Onto business.
Prff..... thinking about this has made me rather sad and intrigued. I'm almost tempted to go around asking people this sorta thing, but I don't know many disabled people aside from basic psychological deficits in my friends, but almost everyone has a chink in the armor, so to speak.
Operating without flesh legs may be interesting to think about, but I don't think it would affect rearing the child too much. In fact, it may make them more open to the idea of human augmentation and limb replacement, which isn't too bad in the long run unless she gets hideous piercings (cheeks, nose, mouth, etc. Think Gauges not rings.) and the only problem I can think off is perhaps kids insulting the offspring about the mother's limits, but if they didn't have that, they'd inevitably find something worse. Of course, the talk may get awkward between Emi/Hisao and the child
As OP said, lack of arms may make holding the baby hard, and breast feeding would also be difficult. I'd imagine some variation of the baby bjorn exists in Japan, so it wouldn't be too hard for the child to be carried by the parent. Of course, the partner could very well just do most of the carrying, and we know from a special someone that object manipulation with legs is quite possible with practice. Breast feeding may be accomplished kitty-style, with the female on her side and the child on its stomach, or perhaps a bit like milking a cow/harvesting bottles of milk. (I should just start making an post script with akll the fanfic hooks I spawn, seriously.) where the child or male "milks" the female to drink/store breast milk. Side effects may include the child growing up more used to bodily openness, but I doubt it. Of course, public breast feeding may be a problem for Hisao in terms of embarrassment, but I'd imagine Rin wouldn't mind the idea, or they could just store it before a trip.
A blind female represents a possible but unlikely danger to the offspring's safety, but I'd imagine that locational awareness would be good enough to perform basic acts of breastfeeding and nurturing if it had been a rather distant that caused the blindness, and the male could help breast-feeding if necessary, either by bottling or directional guiding. It may lead to the child being a bit less reliant on visual cues as description goes, due to the female not describing by looks, and also I'd imagine that the offspring may vocalize more since that is the only way to communicate properly with their mother, something very important early in life. (Perhaps we now know why Misha has some of the less attractive qualities of an air-raid siren...) It is also quite possible, as stated before, that a blind parent may accidentally step on or otherwise not see the offspring, leading to an accident of some kind. However, with proper care and planning, the risk could be mitigated to a below zero percentage, I think. (Not a doctor, just a guy with a keyboard)
A deaf female would present only a couple of issues with child rearing, namely not being able to hear calls for help or similar internal notations, but that could also be resolved with some baby monitors of some sort. It would also not aid in the child's lingual development, however, seeing as it takes two to summon a stork, the male would most likely be able to provide both ASL and English training early in life, perhaps even making them simultaneous reactions to interactions. I couldn't really imagine any other hindrances, but my entire family is introverted so words are only exchanged when needed, and we don't live in a sonically active town either, so I can only say that it may make some culture shock when the child gets introduced to Music etc, but the male could very well stop that.
A physically marred female... presents some difficulties I have no idea what to speak to. Perhaps the child would grow up accepting of other people and their bodies, taking an interest in tattoos from an early age and perhaps being more accepting of that sort of thing.
Hanako's raising of children: As you all have said, it would most likely revolve around over-protectiveness mitigated by her interactions with Lilly and Hisao. (Am I the only one with the Headcanon of the fire happening on or around her birthday?) I think she would also be shy around her child, perhaps prone to withdrawing when the child becomes emotional, or snapping in anger. Without going into highly emotional and theoretical topics about the subject, I also think that she may seek home or private schooling in lieu of the public schools. (American, excuse me if it is different anywhere else, willing to do research for translation for similar concepts in other regions. It's late when I write this.) Furthermore, I suspect she'd be very critical of any actions taken by her child she disapproved of, but may not directly speak to them, leading to a sitcom-esque situation where it all comes out on wedding night for the offspring etc.
My Hisao would not likely be much help in the whole of over-protectiveness, I was bullied as well, so I'm a bit over reactive to the topic when it comes to other suffering because of it.
All of this was written at roughly 12:20-12:40 by a self proclaimed crepuscular INTJ, and as such is subject to both unwillful ignorance on the subject matter and plain dumb wording of ideas. Please debate with me if you feel compelled to, I find it entertaining, but be aware I am stubborn and may not back down on the stated opinions. Take all information stated before this paragraph as an opinion among many, so don't kill me. *eep*