I've never had to pause mid throw in Judo to allow the other guy to take ukemi. In fact in Judo I've never really had to worry about the other guys ukemi, if I'm throwing him correctly there isn't much he can do so there's nothing to worry about. If the guy is half way though uchi mata he can't exactly say "Hang on, stop, lets do this more slowly; I'm unsure of the ukemi." It's a nonsensical thing to say in a judo context, which bit of "tuck head in, try to breathe out" does he not get?
In Aikido though I'm always having to adjust my technique to the abilities of my uke. I can go as hard and as fast as I like with people my level and above but I can't do that with people who are junior to me because I end up hurting them.
I think I see where you're coming from, but have you never had to practice Judo technique slowly? I practiced with a Judo guy one time and he nearly tore my arm out of its socket. At the time I felt that if I had been much of a stiff-bodied person I could have easily been hurt. I've never practiced judo though, so I definately cannot compare the two very well.
My very brief experiences in the Shodokan style reminded me somewhat of a bit of the Judo I've seen online, so I tend to infer a little from that. The waza that utilized relatively less joint manipulation seemed to fit what you describe about Judo. The ukemi seemed to be more straight down to the ground which didn't give uke much time to stop and think...which also seemed to make ukemi just sort of happen as a result.
This relates to my more ki-oriented experiences where my sense was that often I needed to keep a very positive pressure on uke to make the ukemi more obvious. I remember backing off a bit with newer students, but not in a way that allowed them to really adjust a whole lot. For many there was that moment where you could feel them trying to disengage "to take ukemi," and if I allowed them to do that they didn't seem to get better at it. The movement became disjointed and neither of us got the most out of it...again, as I perceived it. So I began to get the sense that I could move slowly to allow uke to feel more of what was going on, but with enough pressure that I still had enough control of their center/body, forcing their ukemi to just happen.
Of course I was never particularly good, so I couldn't always keep the movements smooth enough, but that's where I kind of left off in my approach to "teaching" ukemi to newer students who didn't already feel comfortable being thrown/pinned.
As it relates to "finishing moves," I've the sense that it's just another exercise in continuing the movement. In shiho nage for example I've often done a shomenuchi after uke is pinned, but my feeling was that it wasn't necessarily a strike since it could also be a good transition for switching hands, or extending the elbow back a bit more for stronger uke. Also, in multiple attackers, sometimes you might have to hit a guy while he's down to keep him down longer to afford more time to deal with other people.
I imagine it's also a great way to get the attacker's attention. You don't necessarily have to actually hit them to draw their mind to the atemi-like finishing move.
...Some rambling thoughts about that, anyway.