Speaking from personal, first-hand experience with fatherhood, my answer is a firm "it depends".
If this is pretty much the only thing ZUN does as a "day job", i.e., Touhou games and related works, then I don't think it should be an issue. Especially as he is married, and has a partner to help out (although this makes me wonder: Does she work, or is she on maternity leave? What kind of maternity leave program does Japan have, for that matter?).
However, newborns are pretty much an around-the-clock job. Especially as this is their first child, I'm sure they're both going to have their hands full those first 18 months just learning how to deal with a baby. How well they handle this will depend a lot on the network of relatives around them, or even child-experienced friends who could help, babysit, offer advice.
And of course there's also the fact that kids don't come one-size-fits-all. Their son could be a colicky baby, or be defiant/destructive, or have difficulty with certain foods. These are all normal things, but it's just to say that kids can come with their own individual qualities that can make parenting more challenging.
So really, there's a lot of elements at play here when we talk about what parenthood could mean for Touhou. It depends on many different factors. But I get the feeling it'll continue to chug along - he's said himself he'd make these for his own enjoyment even if the market for them more or less dwindled to nothing - even if at a slower, or more uneven rate.