Yes, although you may need to modify the variant files to allow access to them.
Every function on the SAM3X8E is a "multiplexed" function. That is, it shares pins with other functions. For example CANTX0 is an alternative function on pin PA0.
You can find all the alternative function mappings on page 40 of the datasheet.
You may find that many of these pins already have an Arduino pin number assigned to them in the variant file. If that is the case then you can just use it as you would any digital IO pin.
I have included the comments from the variant files here for quick reference:
/*
* DUE Board pin | PORT | Label
* ----------------+--------+-------
* 0 | PA8 | "RX0"
* 1 | PA9 | "TX0"
* 2 TIOA0 | PB25 |
* 3 TIOA7 | PC28 |
* 4 NPCS1 | PA29 |
* TIOB6 | PC26 |
* 5 TIOA6 | PC25 |
* 6 PWML7 | PC24 |
* 7 PWML6 | PC23 |
* 8 PWML5 | PC22 |
* 9 PWML4 | PC21 |
* 10 NPCS0 | PA28 |
* TIOB7 | PC29 |
* 11 TIOA8 | PD7 |
* 12 TIOB8 | PD8 |
* 13 TIOB0 | PB27 | LED AMBER "L"
* 14 TXD3 | PD4 | "TX3"
* 15 RXD3 | PD5 | "RX3"
* 16 TXD1 | PA13 | "TX2"
* 17 RXD1 | PA12 | "RX2"
* 18 TXD0 | PA11 | "TX1"
* 19 RXD0 | PA10 | "RX1"
* 20 | PB12 | "SDA"
* 21 | PB13 | "SCL"
* 22 | PB26 |
* 23 | PA14 |
* 24 | PA15 |
* 25 | PD0 |
* 26 | PD1 |
* 27 | PD2 |
* 28 | PD3 |
* 29 | PD6 |
* 30 | PD9 |
* 31 | PA7 |
* 32 | PD10 |
* 33 | PC1 |
* 34 | PC2 |
* 35 | PC3 |
* 36 | PC4 |
* 37 | PC5 |
* 38 | PC6 |
* 39 | PC7 |
* 40 | PC8 |
* 41 | PC9 |
* 42 | PA19 |
* 43 | PA20 |
* 44 | PC19 |
* 45 | PC18 |
* 46 | PC17 |
* 47 | PC16 |
* 48 | PC15 |
* 49 | PC14 |
* 50 | PC13 |
* 51 | PC12 |
* 52 NPCS2 | PB21 |
* 53 | PB14 |
* 54 | PA16 | "A0"
* 55 | PA24 | "A1"
* 56 | PA23 | "A2"
* 57 | PA22 | "A3"
* 58 TIOB2 | PA6 | "A4"
* 69 | PA4 | "A5"
* 60 TIOB1 | PA3 | "A6"
* 61 TIOA1 | PA2 | "A7"
* 62 | PB17 | "A8"
* 63 | PB18 | "A9"
* 64 | PB19 | "A10"
* 65 | PB20 | "A11"
* 66 | PB15 | "DAC0"
* 67 | PB16 | "DAC1"
* 68 | PA1 | "CANRX"
* 69 | PA0 | "CANTX"
* 70 | PA17 | "SDA1"
* 71 | PA18 | "SCL1"
* 72 | PC30 | LED AMBER "RX"
* 73 | PA21 | LED AMBER "TX"
* 74 MISO | PA25 |
* 75 MOSI | PA26 |
* 76 SCLK | PA27 |
* 77 NPCS0 | PA28 |
* 78 NPCS3 | PB23 | unconnected!
pin 4 connected to both PA29 and PC26andpin 10 connected to both PA28 and PC29. – Jack Jan 08 '20 at 13:18If there is a number assigned in the variant files then you can just use that as you would for any other digital pinif you may include it in the answer. Also a link to the variant file for the lazy people that might read this thread – Jack Jan 08 '20 at 13:24