I am designing an acquisition system that has two parts, a hub and an acquisition part that collects the signals. The two parts communicate through FPGA Serdes.

The hub has a main clock from 16MHz crystal oscillator later multiplied to a higher frequency and the acquisition part has another FPGA that I am trying to choose a crystal oscillator for. The two parts are connected through long shielded cables and share the same power, my question is what considerations should I keep in mind for choosing the frequency of the second oscillator? does it have to be within the 16MHz range or around 20MHz.

The reason for this is because the system has to pass EMC and I am afraid if the crystal frequencies are close, this can cause strong harmonics problem in radiated or conducted emission. Therefore, what are some design considerations for EMC when choosing multiple crystal oscillators in a design.

TL;DR: if you don't have to worry about EMC from each oscillator separately, and you're not doing something really odd, you don't have to worry about them together.

"Harmonics" is a single-source thing: one periodic signal is, or is munged into, something that isn't sinusoidal.  That can only happen if it has harmonics, and the harmonics are higher the sharper the edges on the periodic signal.

In theory you could have some signal mixing between the crystal timebases, but I'm counting that as "something really odd" -- and if it happened between two 16MHz crystals, it'd happen between a 16MHz and a 20MHz crystal.

Do worry about getting your EMC right.

Don't worry about the timebases interacting.