Is it possible to use the Arduino Due's specials pins for digital writing and reading?
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!