I can share some data points here.
I have a team of 6 guys. We all had older 12-core mac pros with various graphics cards (mostly the old ATI cards that could drive three monitors although we also had a couple with aftermarket Nvidia cards). Three of us were running 3 x 30" monitors (using DVI or MDP->DualLinkDVI). One was running 2 x 30" (again with MDP->DualLinkDVI). Two were running Apple 27" monitors.
None of those old Mac Pros were affected by the 10.9.3 upgrade. All kept humming along with 1, 2 or 3 monitors.
Yesterday, we received 6 brand new Mac Pros (2013). One of us upgraded to dual 4k monitors using MDP->DP cables... that's working fine. Two of us were still wanting to use 3 x 30" using MDP->DualLinkDVI adapters... but only _two_ monitors will work that way! The guy using 2 x 30" monitors via MDP->DualLinkDVI is just fine... and the other two using single 27" Apple monitors are fine.
To summarize: we cannot run more than two 30" monitors from MDP->DualLinkDVI adaptors on the new Mac Pros.
However, we noticed that one of the two guys affected by this bug has a newer set of monitors that _do_ have DisplayPort on them. So we jacked his 3 x 30" monitors into his new Mac Pro using MDP->DP cables... and it works perfectly!
All in all... we paid over $45k for these machines... and I'm surprised to see this much trouble with trying to use monitors with them. One guy is currently sitting in front of 2 working monitors and 1 blank one. I haven't contacted Apple yet... but I am going to do that soon.
I hope 10.9.4 lands soon...