Depending on your motherboard, by installing a 2nd 16x video card may rob some of the PCIe rails from the original 16X slot, making them both act like PCIe 8x.
Will this be noticeable? Probably not, it depends on other unknown/dynamic factors.
Alternatively, you may want to look into getting a couple DisplayLink USB video adapters for "cheap and easy". They use a bit CPU power, but again, it may or may not be noticeable depending on your personal usage.
You can also just unplug them if you need more power (on less monitors).
If you haven't bought the monitors yet, you can get DisplayLink-enabled monitors which allow you to just plug the monitor in via USB (and chain them if you'd like), skipping DisplayLink dongle(s).
Most of the current ones seem to be aimed at mobile (~7"), but i know Samsung was making a 22" for a while (for example).