Because of the components of bitumen-based shingles, degrees of deterioration can normally be seen at various stages in their life cycle. Most older shingles had a paper base (often referred to as felt) that was saturated with tar-like bitumen and topped with coloured granules. Newer ones usually have a fibreglass base that is supposed to be stronger and longer lasting than felt. Otherwise the overall composition is similar. The granules help reflect ultraviolet (UV) rays, extending the life of the shingles. The tops of the shingles are not granulated, to allow for easy bonding to the next row of shingles with a small adhesive strip, activated by heat from the sun. Aging of shingles can be attributed to deterioration in one or more of these components.
On older roofs, shingles are seen to begin aging when granular loss is observed. This may be observed by excessive debris in the eavestroughs, dullness in the overall appearance of the roofing, shrinking of the individual shingles or curling at the bottom edges. As the bitumen erodes after years of exposure to UV light, rain, snow and other environmental factors, the underlying felt or fibreglass mats appear to shrink. The keys at the bottom of three-tab shingles get wider and often curl upward, exposing more of the underlying layer below. The discolouration of your shingles may be because of this granular loss, an underlying defect in the shingle or environmental conditions.
As shingles lose their granules and begin to deteriorate, some changes in appearance may occur. Dark-coloured shingles may fade, and light-coloured ones may darken with dirt or debris, with more of the dark-coloured bitumen exposed. Neither of these issues are particularly problematic, and if that is the cause of the dark areas on your roof, there is nothing to be concerned about.
Also, debris from nearby vegetation can cause various areas to become discoloured. If you have lots of trees near the roof or overhanging, sap dripping from the trees will often cause stains on the roofing. This can be minimized by washing the roof with a garden hose or with a pressure washer on a low setting, but care must be taken not to damage the shingles when cleaning. The roof should always be washed from the top down to prevent driving moisture under the shingles, which may cause damage and leakage.
You are correct that a lack of proper attic ventilation can cause premature deterioration to shingles, but this is normally seen by curling, lifting or shrinkage. Faint changes in colour or visible cosmetic defects are not really a symptom of that defect. While you should look in your attic and on your roof to ensure the vents are adequate and not blocked by debris or excessive insulation, I doubt this is your issue. Periodic inspection of these areas is always a good idea, but will likely not provide much insight into your problem.
The next thing to consider is environmental conditions in the area where your home is located. Are there any unusual industrial sources, such as power plants, factories or refineries nearby? Pollutants emitted from these sources could cause discolouration of your roof from chemicals in the air. Various forms of airborne pollutants can cause roofing or other house components to discolour of deteriorate.
Do you have a wood-burning appliance in your home or nearby? Soot particles from fireplaces and wood stoves will often cause dark staining on roofing, particularly light-coloured shingles. Again, this may be mostly cosmetic in nature and not something that needs any major remediation.
Finally, a defect in the manufacture of the roofing is the other possibility. Various manufacturers over the years have produced shingles with various deficiencies. These may range from de-lamination of laminated shingles, excessive granular loss, curling, cracking and other forms of premature wear. While it is difficult to accurately assess whether this is occurring, a slight discolouration on the shingles would only be a minor concern. If you are seeing excessive curling or shrinking along with the dark spots, more serious evaluation may be needed.
While serious premature wear and deterioration to bitumen-based shingles is something to be investigated and fixed, slight discolouration may be nothing more than a cosmetic issue. Differentiating between the two will be important to determine whether any remediation is needed, and I doubt your issue will be little more than a visual one.