Hi there @umutgemisi,
As ard_newbie has commented you can use library tc_lib just for measuring digital signals.
You can find tc_lib at: GitHub - antodom/tc_lib: This is a library to take advantage of different functionalities available on Timer Counter (TC) modules in Arduino Due's Atmel ATSAM3X8E microcontrollers
@HermannSW (thansk HermannSW) has already done some testing to know the limits of tc_lib. In this post you have a summary:
https://forum.arduino.cc/index.php?topic=393842.msg3086694#msg3086694
I think they can help you to have a better idea about tc_lib, they report measurements of signals with frequencies greater than 20Mhz.
As to if tc_lib can capture different signals in different pins simultaneously, it can, just have a look to the library's documentation.
I hope it helps.