Your link discusses how a CCD (charge coupled device) image sensor works. Note, CCDs have applications besides images sensors, but the vast majority of CCDs are used as image sensors, and that is the only primary application I will be discussing.

CCDs

In typical CCDs used for color image sensing each CCD cell has a color filter over it. The most commonly used pattern groups 4 cells together with one red filter, one blue filter, and two green filters. These filters only allow photons of their corresponding colors, in a certain frequency band through. A greyscale CCD just doesn't have these filters.

A CCD (when used as an image sensor) at its core is a photon counting device. A photon that is incident upon the active region of a CCD excites an electron through the photoelectric effect which is then stored within that cell of the CCD. This process continues as long as photons hit the cell causing electrons to accumulate within each cell.

Your camera lens projects an image of the scene you are taking a picture of onto the CCD. This is the same as in a film camera, except with film instead of a CCD. Each pixel corresponds to one cell within the CCD. In the case of a color image, each pixel is the the product of one or more filtered cells, depending on the algorithm and cell location. The simplest algorithm groups each set of 4 filtered cells into a single pixel. However it is common for interpolation schemes to increase the number of full color pixels to equal the number of CCD cells.

Photon Energy Dependence

The signal does depend on photon energy, but only as a threshold. In order for a photon to generate an electron through the photoelectric effect it must have a certain amount of energy. This amount of energy is the "bandgap" energy of the semiconductor. The bandgap energy of silicon is about 1.1 eV, meaning photons with a wavelength of about 1100 nm and lower will be detected. As you continue to increase photon energy the signal remains constant at one electron per photon. Once your photons have twice the bandgap energy, or more, an incident photon can generate two electrons, but it is fairly rare.

Once you have decided you are done taking your image the shutter is closed and it is time to read out what image was captured in the CCD. To read out the image the charge within each cell is shifted over one column within its row. The first column is then read out. This can be done by either measuring the current to discharge the cell, or measure the voltage of the cell while knowing the capacitance. Both of which can tell you how many electrons were stored in that cell. After the first column is read out, the cells are all shifted again, and this repeats until all cells have been read.

Non-Idealities

There are a number of factors that prevent typical CCDs from giving you an exact photon count. There is a significant amount of thermal noise that can only be reduced by lowering the temperature well below what is reasonable for a handheld camera to be capable of. There can be leakage within the CCD cells which can cause electrons to escape the cell, or move into nearby cells, which prevents an accurate count. There will also be photons that reflect off the cell, and therefore aren't counted.

However, none of this changes the fact that a CCD counts photons. It just means it isn't a very precise photon counter. More on this below.

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Does a CCD Count Photons?

I believe it does, but it comes down to the definition of "count". Lets consider an analogy.

Alice, Bob, and Chris each own an apple orchard. They want to know how many apples have fallen off the trees in their orchards. To do this they use a Tennis Ball Coupled Device (TBCD). It might look like an ordinary basket, but trust me, its a TBCD. Alice, Bob, and Chris walk through their orchards putting a tennis ball in the TBCD for each apple they see on the ground. By the time they have finished, each has a number of tennis balls in the TBCD equal to the number of apples that fell off the trees.

To figure out how many apples fell off the trees, Alice, Bob, and Chris each use a different method. Alice proceeds to count out the number of tennis balls in her TBCD. When she is done, she knows exactly the number of apples she saw. Bob is not as patient as Alice and uses an advanced computer vision system to automatically count the apples in his TBCD. When he is done, he knows approximately the number of apples he saw, but there is a small error because the CV system isn't perfect. Chris can't afford such a system, nor is he as patient as Alice, so he weighs his TBCD and using the weight of a tennis ball can determine approximately how many tennis balls there are.

Now here is the question. Who of these people used a system that counted the number of apples that fell in their orchards? Each at one point had a number of tennis balls equal to the number of apples. Does the readout method impact whether or not the TBCD counts apples that fell onto the ground?

The TBCD is (unsurprisingly) directly comparable to a cell in a CCD. It stores a number of electrons equal to the number of photons it captured. This most certainly qualifies as a photon count. Then, depending on your readout circuit, you might get a more or less precise reading of this value. Is it a count? If my image sensor counts the number of photons, but doesn't tell anyone, did it still count the number of photons? As I said earlier, I think this comes down to your definition of count, but I believe a CCD qualifies as a photon counting device.