Interesting....
I, too, filed a bug report with Apple as soon as I ran into the third display not working issue on my nMP and 10.9.3.
In my own situation, my configuration consists of 3 idential 27" LG monitors running at 1920x1080 resolution.
I have one attached directly to the HDMI output on the back of the nMP, a second using a standard "pigtail" type connector that goes from Mini DisplayPort to HDMI, and a third using Apple's Dual Link Mini-DP to HDMI adapter (the $99 one).
It all worked great in 10.9.2, but after upgrading to 10.9.3 and losing my third display, I tried many combinations of plugging things into different ports to no avail. I could always get 2 displays to work but not the third.
In my case, Apple Engineering just requested today that I take a photo of how everything is hooked up in the back of the machine and send it to them. (They haven't yet closed out my ticket as a duplicate.) I'm thinking at this point, they're just collecting data on various configurations of displays and adapter types that are failing?
I don't have the option of using straight-through Mini-DP to DP cables because my LG displays don't have Displayport connectors on the backs of them. (They only have VGA, DVI or HDMI.) I think I do have a Mini-DP to HDMI straight through cable around here someplace, though. I wonder if anything would change if I tried using that in place of the display connected directly to the HDMI port on the back of the nMP?
For now though, I used Time Machine and rolled back to 10.9.2 ... so I may just wait and see if Apple gets this fixed by the end of the week.