When you hardwire something it become integrated into the board.
Hardwire:
"To implement (a capability) through logic circuitry that is permanently connected within a computer and therefore not subject to change by programming."
All cyberdecks have one slot that accept one module.
The module in the cyberdeck module slot is not hardwired/integrated into the board.
"Inserting, removing, or swapping modules requires a Hardware + Logic [Mental] (1) Test and about half a minute of time (10 Combat Turns)."
An integrated module is a module that is hardwired into the board (the alternative would be a module you can insert, remove or swap).
Devices (including but not limited to cyberdecks) can only have one module hardwired/integrated into the board.
"Most devices can only have one module, although cyberdecks can have two—one in the normal module slot, and the one you hardwire in".
(they are not talking about "one modification" here - they are talking about one hardwired module + one module in a cyberdeck module slot)
The form factor EvoTech Himitsu Commlink already come fitted with a module. This module does not come in a cyberdeck slot. It come hardwired/integrated into the board.
"the commlink has a stealth module integrated into the board"
There is no specific rule that say this hardwired/integrated module would not count towards the general rule that limit all devices to one hardwired/integrated module per device.
There is no specific rule that say this commlink can accept two hardwired modules.
In the chapter "The guts of of the matrix" they frequently use the word "module" while actually talking about the key word "cyberdeck module".
Two pages earlier, still in "The guts of of the matrix", they also use the word "module" in the description of the EvoTech Himitsu.
They might or might not mean a "cyberdeck module" like the other ~20 times they used the word "module" elsewhere in "The guts of of the matrix".
They might or might not mean a different concept that is also named "module"
(this is similar to SR5 when they in some cases meant the key word "cyberprogram" but in many cases just typed "program").