scholargipsy asked "do you believe, as some aver, that all babies are adorable, or do you think there's such a thing as an ugly baby/toddler? If the latter, how do you pay compliments to a child who has not, as yet, not manifested agency or personality, when it's manifestly unattractive?"
My first thought is literary--a passage from Anne of Avonlea:
"What will we say if the baby isn't pretty?" whispered Diana in trepidation as they followed the excited Lorenzo into the house.
"Oh, there will certainly be something else nice to say about it," said Anne easily. "There always is about a baby."
And that's about where I stand on the matter as well. But to answer the questions more concretely:
No, all babies are not adorable. There's another Anne Shirley quotation about how every baby is a miracle and that certainly has a ring of truth about it (dude! people can grow other people! craziness!), but they are not all adorable. I actually have a theory that babies fall into different categories defined by what other living creature they resemble. There are the babyish babies, of course, but there are also tomato babies (red and scrunchy), old man babies (when you can see exactly what they're going to look like at the final toothless and diaper-full phase of their lives), monkey babies (ooh ooh!), froggy babies (often interchangeable with alien babies) and some other categories I'm sure I'm forgetting. I have learned that people get very offended when you categorize their children this way, though, so this tends not to be my approach in commenting on a baby's appearance. Which is about the only thing you can comment on when the child has not, as you say, manifested agency or personality. So, on to your question:
The thing to remember here is that paying compliments to a baby is not actually paying compliments to a baby. It is actually paying compliments to its adult(s). As such, you pick something that will resonate with the adult(s), something that shows you are paying attention, that you see something they also see and admire in their child. Certainly it can be a general descriptor--adorable, beautiful, inquisitive--but it can just as easily be something specific--a precious mouth, gorgeous eyes, charming expression, etc. Anything that shows you really took the time to notice this creature with which the grown-up is (in the best of times) so very smitten or (in the worst of times) desperate to make a connection with. Something that tells them that, if it is a good day, the swelling pride they feed is justified or, if it is a bad day, there is something that makes the exhaustion and frustration worth it. I'm making this next part up as I go, but I think there's something in it: parenthood can be such an isolating thing that the point of complimenting new children is to make the parent feel connected, less alone. That they're not crazy. Even though they kind of are.
This is the thing about new babies--although most of the adults who come with them know that other people are unlikely to be as consumed (smitten and/or overwhelmed) by (hm, that phrasing has a funny taste to it) the child as they themselves are, they still tend to overestimate the interest that other people have in it. So, basically, anything you can do to support the illusion that their baby is as perfect as they think it is or want it to be generally goes over well. And I say this three years out from my own newborn experience (thank you, by the way, for attempting to butter me up with obligatory praise of my child's obviously beauty...) and, more importantly, having come to the realization several months post-postpartum that my newborn was perhaps not quite as adorable as I believed her to be at the time. Sacrilege, I know, but I clearly remember a moment when I suddenly saw my biases more clearly. (Acne? What acne?) Or maybe it was just a matter of comparison--personality most certainly gave me more to admire in the child.
Which brings me to the other thing I'll say about your question: kids manifest both agency and personality long before they become toddlers. And at this point it becomes much easier to pay compliments. I do, in these instances, make a concerted effort to avoid general descriptors of the appearance (gorgeous, handsome, etc.) and focus on personality, behavior, and experiences. Babies have all those things, and it's quite easy to notice them once you're paying attention. But that's straying from the heart of your question, isn't it? You want to know what to do when the kid is really really unattractive. When you can't find anything specific to comment on, be vague and supportive. Compliment the situation (you have a baby! how wonderful! look at that face! babies are so sweet when they're sleeping, aren't they?), the outfit/accessories (that may be a cop-out, but honestly, clothes really do make the kid some days), or the parent (you look so happy! it's so wonderful to see you out and about! you have a lot to be proud about!), or address yourself directly to the baby (I'm so happy to meet you, baby! I've heard such wonderful things about you!). Give the adults something to hang their parenting/care-taking hat on or to interpret in a way that suits their needs. Find something true and kind. Or lie and hope they're too sleep-deprived to notice. But you shouldn't have to. There's always something nice to say about a baby.
Note to anyone with children, now, then, or in the future: Resemblances between compliments cited above and compliments given in real life are purely coincidental. Your baby is AMAZING and NOT AT ALL UGLY. Except maybe when it makes that face. You know the one I mean.