For sure the biggest issue is the canopy you are taking photos through – it will have reflections and possibly scratches, which you possibly (probably) will not see until after you get back on the ground. The only solution to this is to take absolutely loads of shots and hope one is OK or can be cropped to a good image on you favorite photo-app when back on the ground.
Regards, SD..
It much depends on how your plane has been looked after. I’ve had mine since 2002 and have been the only pilot nearly the whole time; certainly since 2006. If it was an 18 year old rental or syndicate plane then it would be very different.
There may be some polish which can work temporarily to fill in scratches. I suspect Plexus does this to some extent, with very fine ones.
I tend to just open the windows. However when I got my aircraft it did have a scratch (not very deep but annoying enough) from part of a window lock mechanism left on. After asking around I tried a bit of peek metal polish which worked a treat and totally removed it. I haven’t noticed any optical clarity difference, but haven’t looked in detail. I was more than happy with the fix.
Not many types can have windows open 
On a TB you are likely to get the door departing the hinges and possibly taking out the vertical stabiliser, with fatal results. As a minimum there will be very expensive damage (4 digits plus; I’ve seen it done on the ground by wind).
The older TBs have a little window on the left door which many find quite useful and you can shoot through that, but the angles are limited.
If a camera is focused on infinity, and is set to a reasonable aperture for a good shutter speed (say less than F8) then it won’t see scratches. However, scratches will show up as a reduced contrast; much more so if there is sunlight hitting that window surface.
What gets more difficult is shooting through the propeller. Then you need a slower shutter, say 1/80 to completely remove a prop running at say 2500rpm, and to get 1/80 without overexposing you need a smaller aperture (say F16). Or use a neutral density (ND) filter but that’s a hassle, even if your camera can take a screw-on filter. And scratches then show up more.
I’ve had a Cessna window depart when opening in flight (it was on my Cessna 140 in Houston, the window ended up in Galveston Bay). Normally you’d open it fully and it would lie against the bottom of the wing, but this time, it opened a bit, fluttered, then departed the airframe…4 days before we were supposed to fly to Oshkosh!
We did get a replacement in time.
The Auster has sliding windows (similar to a Mk.1 Mini) which don’t have this risk, but can’t be opened as wide – but usually fine for taking photographs.
Zlin 26 series is a great airplane also for aerial photography – just sit in the front seat and slide the canopy a bit. If properly maintained it will not slide fully and you have great view. Just make sure the guy in the back at controls is “well” dressed. The attached picture is an example. taken back in 2010, Canon 350D, no image stabilization at all.
