Yeah this type of behavior is pretty common among Japanese people it seems.
One thing that helps is to make the meetup location near your house - I have one friend who doesn't even leave his house until his date messages him and tells him she's arrived to the station for this precise reason.
Another thing you can do is just assume they're kinda spacey idiots (which in a lot of cases, they kinda are) and remind them the day before. But do it in a way that doesn't seem like reminding or confirming.
Example
Bad:
Are we still on for tomorrow?
Soooooo are you coming?
Can you still make it tomorrow @ (x time)?
Hey, don't forget our date tomorrow!
Better:
Leave out one piece of information (such as the exit of the station, or exact meeting place)
"So tomorrow, it's exit 6b at 6pm!"
"Looks like rain tomorrow.. bring an umbrella!" <--- helps to reduce rain-day flakes since it seems like attractive J girls are like the wicked witch of the West and melt in the rain
This way, you can "remind" her without it seeming like you regularly get stood up / are worried she actually will flake (which creates a self-fulfilling prophecy .. she behaves how you expect her to behave)
I always recommend to be doing something you want to do even if you have a date planned. So, if you want to meet in Shinjuku, head over to the bookstore and grab that book you wanted right before your date. If she cancels, you don't mind as much because you were there anyway. Or , if you like street game like me, whenever someone cancels on you, just meet 10 more girls and find a cooler chick!!