Probably. I have not made direct measurements, but FAA is a strong fixative that alters many cell components. If you want to avoid artifacts I suggest you using a more gentile fixative such as glutaraldehide.

Stomata counting and measurements were done on excised epidermis of leaflets (n = 10) and fruits (n = 10) fixed, and stored in FAA (formalin: ethanol 50%: acetic acid, 1:1:18, v/v). Epidermal fragments (~1 cm2) were peeled off for 24 h, at 60ºC, by Jeffrey's method stained with 1% safranin in 50% ethanol, and mounted in glycerin jelly (Johansen, 1940). Photographs were taken using an Olympus SZH photo-microscope. Stomata density were measured using an Olympus BH2-DA drawing attachment connected to an Olympus light microscope, and measurements of stomata pore area (n = 50) were made using an image analysis software (Motic Ihe stomata pore area of fruits of D. miscolobium was larger than that of leaflets, but due to lower stomatal frequency, the fraction of fruit epidermis surface area occupied by stomata pores (Ast/A) corresponds to just 9% of the Ast/A of the leaflet abaxial epidermis . The difference in Ast/A between fruits and leaflets resulted in the lowest conductance values being observed on fruits. In the morning measurements, fruit conductance, 29 ± 4 mmol.m-2.s-1, corresponded to 7.8% of that of leaflets, 378 ± 165 mmol.m-2.s-1 , which were similar to the leaf conductance of three other cerrado woody species in the wet season (Lemos Filho, 2001). In the fruits, the lowest values of stomatal conductance were constant during the day. The patterns of D. miscolobium leaflets were similar to those observed for Qualea grandiflora, another cerrado tree (Franco and Lüttge, 2002). The maximum conductance values occurred early in the morning, followed by a continuous decrease at noon, with a small recovery around 2:00 pm, and an expressive decrease in the afternoon, with the lowest incident light values .mages 2000- Canada).

yes, they will definitely change as they are very sensitive. Other alternative to check the stomatal opening is using of Infra red gas analyzer

I thing that If you fix with FAA the stomata opening change because FAA is a very strong fixator

It sure will. Stomata close upon drying, it's the water pressure that maintain it opened. Even little changes in light and temperature for a few minutes cause changes in opening. If you want to evaluate leaf porous area, which is the sum of the stomata pores areas, there are proper methods to do so. I think the simplest way I've heard of is to use a colorless nail polish to cover a little part of the leaf area, which will, in theory (excuse-me, I didn't do it myself) register the stomata condition. Afterwards, you would peel this film and observe in a microscope. (Here is a very basic tutorial: http://dtc.pima.edu/blc/1004thed/004/004_Leaves_Stomata/stomata.html). Afterwards you can register and measure the stomata using a proper software (ImageJ is a good freeware option). measuring a few stomata will be sufficient for a good statistical analysis. After you have the average opening, you just multiply for density and leaf area. I suppose it will give you a decent estimation. Just remember that stomata density varies in a single leaf and also between leaves. For example, sun leaves usually have more stomata (see this link: http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.2011.00124.x/full)

If you are only interested in length of stomatal complexes and stomatal density all the mentioned methods should work fine.

Actual stomatal aperture, however, depends on the belance between guard cell and epidermal turgor. Any change in transpiration rate and water supply supply to the leaf will rapidly change this balance and result in hydropassive movements. This applies to any fixation method and any method to make imprints. I would only trust these measurements after proper evaluation of these artifacts. These errors could, however, be acceptable depending on the question and your experimental design. Please note that such hydropassive effects can vary between species (depending e.g. on rigidity of leaf tissues) and can vary largely with leaf water status and transpiration rate at the time of sampling.

I would say even if there are influences of FAA, your different treatments are exposed to the same changes, so if you do this comparison, it should be working fine. But there are papers say spreading nail polish to part of the leaf, take the thin film off by adhesive tape. Then you can see the stomata under microscope. I did this before, it is good to measure like stomatal length, width and density and pore area. To spread the nail polish well needs some practice, try to cover the leaf surface evenly to avoid error brought by artifacts. BTW, nail polish is harmful, the covered leaf will get dark afterward. Hope it helps.