NodeMCU ESP8266

Do flash uses GPIO6-11 all the time? Can we use any of these pins for our purpose? What if someone needs an SPI communication, as these pins are locked by flash.

It is Quad SPI. The CS pins for this SPI interface are controlled by low level code. So you can't use this pins as GPIO and they have limited use as SPI too. If the flash access is set to normal SPI, the two pins io 9 and io 10 used for quad mode can be used as GPIO.

Can I use GPIO-0 (flash pin) for my purpose, as after flashing the MCU the pin will get free.

You can use io 0 as GPIO. Only make sure it is HIGH at boot. The bootloader reads it at boot to determine if it should go to flashing mode. Other boot config pins are io 2, it must be HIGH at boot and io 15, which must be LOW at boot.

Do CP2102 uses GPIO 1 and GPIO 3? Can I use these pins for my purpose? (Given I need the data via USB, which I guess comes through CP2102)

Pins io 1 and io 3 are wired to the USB chip and used for Serial. They can be used as io pins, if you don't need Serial communication over them. Serial in esp8266 Arduino can be swapped to different set of pins for use with a serial device. For output printing you can use Serial1 which has only TX. To relay this output to USB bridge io 2 (Serial1 TX) to io 4 (Serial TX wired to USB).

Can I receive the sensor data from SoftUART bus and get that data to my computer via USB?

You can use SoftwareSerail or the trick mentioned above.

see NodeMCU pins