Yes, it would be beneficial if you are angling the AP correctly (second AP would be up and to the right), even with the antennas on the other AP being vertical. If you angle this the wrong way (second AP is up and to the left), then you will be making things worse.
This type of antenna produces a signal pattern in a toroid or doughnut shape (with the antenna forming an "axel" through this pattern).
Angling the one would increase the energy that arrives at the higher AP and will allow for slightly better reception by the lower AP.
However, this may only be true if all you are concerned about was the signal between the two APs. If you are providing service to other devices from the lower AP, this could negatively impact the service to those other devices.
If it is only signal between the two APs, then I would question why you are using omnidirectional antennas over directional? Even if the higher AP is serving multiple lower APs, if the lower AP only connects to the higher one, it would be better served using directional antennas. If all the APs are lower than the higher one, then I would look for antennas with "down tilt" for the higher AP if possible or else something like a patch/panel pointed downward.
With any wireless, you should make sure to understand the signal patterns of the antennas you choose.