This doesn't have to be a crunchy mechanic.
Rather can be considered a "seasonal" mechanic, since for two particular systems it happens at different times of the local system "year".
So, it could be something similar to a "trade wind" mechanic where the trade winds performed differently (and thus lengthened or shortened particular trade routes) during particular times of year. I don't know if our actual trade winds manifested something like that or not, but it's still a useful analogy.
Because this isn't something that changes daily. Once shadowed, the planet will stay shadowed for some time. Much like the length of day changes seasonally, the length of travel will slowly lengthen day by day until it reaches some peak and then it shortens.
Now, there is a complicating factor that as the two systems orbit at (likely) different speeds, you have the shadows of both systems to deal with. But the overall point is that the travel times can change like the tides, astrogators would be well aware of this, and it would simply be a normal circumstance of trade.
"Oh it's winter there and summer here, so we need to add a week to the shipping time." This adjustment is something that can be handled by referee fiat without having to do any number crunches.
When System A is in Spring, add 2 days. In Summer add 1 day, fall and winter, zero days. Same with System B. If A is in Spring and B is in Spring, add 4 days. It varies by M-Drive, and perhaps my estimate of days is wrong, but that's the gist of it.
Give each planet a note as to which season is in which month, and go with it. System A has Spring from May through July. System B has Spring from October through December. Go to each system and roll a D12 for the "Winter start" month and go from there.
They don't even have to be out of sync with each other (i.e. where one systems year is faster enough than the other that they get out of sync from one (or more) year to the next). Since most habitable worlds have similar orbits, they'll have similar periods to where over the span of 5 years, there will be little overall change in these delays from year to year. So, set it up once, make a note for each system, and then just keep track of the month, and be done with it. You get the flavor, you get the impact, and all of the math is gone, and it takes maybe a 1/2 hour of time to set it up once for your cluster of worlds.
It also gives faster (Higher M-Drives) traders a distinct advantage as the non-jump space time of travel becomes more a factor in the overall shipping time during bad seasonal delays.