VGA is an analogue connection, which means that it cannot support higher resolutions. There is a slight possibility that you won't be able to run your monitors in their native resolution if you switch one of them to VGA. I'd suggest getting a VGA->DVI adapter for the conference unit.
Just 1 question though: Are all 3 outputs from the video card? If one is coming from the back of the motherboard, then it is from the integrated graphics which means that you won't be able to use all 3 of them at once.
The card does not support 3 independent outputs simultaneously. The ones that do require displayport. Vga typically supports up to 2048x1536. You most likely will not notice a difference at your res. Vga to dvi is still limited by vga's bandwidth.
*You can use igpu at the same time depending on the chipset.
Many cards support up to three DVI-D/HDMI outputs without Displayport. Most do not, but there are many that do. Also, I don't think that OP would have a problem using a VGA output as a third output if those DVI ports are using digital signalin. The problem with using more than two DVI-D/HDMI outputs simultaneously on most cards is that most cards only have two HDMI/DVI-D *lanes* and since VGA does not use such a lane, just like Displayport (except VGA is analogue instead of digital), it should work even when there are two digital DVI-D/HDMI lanes in use. I might be able to scrounge up enough cables and displays to give it a try later.
Regardless, OP, there probably won't be much of a difference between switching one of the monitors to VGA. I've used a similar display to yours with both DVI-D and VGA and I didn't notice a difference between the two in picture quality.