arding my application, would there be a more efficient way?
You could try to reach the speed with just 1 board. however your specifications are not detailed enough yet. A few Khz is rather vague.
The "sensors" are quadrature encoders of a master/slave setup.
sensors = how many 2,4,6?
What do you mean by master slave setup?
=> sounds like an attachInterrupt() job.
IIRC An SD card performs best if you can write a sector/block at a time (256 bytes) so if you buffer up in RAM until you have a full sector (optionally padded) you can write that directly to SD card. For details of performance browse the storage section of the forum (e.g. the work of fat16lib).
I expect this is almost as fast as using 2 Arduinos while easier to build.