I'm not really sure if it makes a difference or not. I do recommend taking your water samples from whatever point of your system is farthest from the fish tank though.
I think that only pH is the one you should really be concerned with (time of day), since things like algae (and CO2 respiration) will cause a diurnal swing in pH (twice a day). So, that difference in pH can throw you off. On the same token, night time algae die-offs might influence NH4 readings, but I highly doubt it would be of significant concern. (To what degree, and if NH4 would even fluctuate much, probably depends on some set and settings specifics, but I'd only worry about time of day pH testing really).
For the ammonia test especially, you want to test water that is not coming straight from the fish tank because you will get an accurate assessment of how much ammonia is actually in your system. In the fish tank, the fish are constantly giving off ammonia, so if you test your water from the tank, your ammonia reading will be higher because it has not had a chance to go through your biofilter (grow beds) yet. You want a reading that shows if all your ammonia is being taken care of or not.
Well Peter at any time of day the pH reading will be accurate. Meaning it will accurately reflect the current pH of your water at that given time of day...
Take a pH reading at dawn, then take one in the late afternoon. If there is a marked difference it's often because algae will 'use up' a lot of dissolved carbon dioxide during the day in order to grow, but at night it will use up dissolved oxygen and give off carbon dioxide. Carbon dioxide dissolved in water is an acid (called carbonic acid...H2CO3) and will affect the system pH giving you a lower pH reading at dawn.
So, the pH of a system with a ‘significant’ (relatively speaking) algal presence increases with photosynthesis…algae continue consuming carbon dioxide faster than it can be produced by bacterial respiration. As CO2 diffusion from the atmosphere is minimal, primarily due to elevated surface water temperatures and the fact that we often heat our water in the winter time, the CO2 deﬁcit during peak photosynthesis is met from the dissociation of bicarbonate ions. This bicarbonate dissociation with concomitant consumption of CO2 by algae, increases the concentration of hydroxyl ions in the water column causing the pH to rise. Which is why you will get a higher reading in the late afternoon. But both readings are accurate....since they both reflect what is going on at the time.
Take both readings and do what you can to block out excess sunlight/light from ever hitting the water (to keep algae down)...
Hope this helps. I tried to be as 'definitive' as I could...and hopefully not just confusing
Btw...this dissolved CO2 thingy is also why you will ALWAYS get a lower pH reading when testing the water straight out of your tap, than if you let that same water off gas CO2 for a couple of days before testing it. This is a case where we could speak of the term "accuracy". The water that sat out in a glass for a few days will give you the accurate and true pH baseline reading of your source water...
I like testing approx 2 hrs after feeding(assuming you turnover the FT once per hr) to see how much ammonia in in the system. The second ammonia/nitrite test after 12 hrs to see how much the system is "digesting" it, i look for a close to zero reading here. As my 12 hr reading starts approaching a 1ppm reading, i know to its time to reduce the feeding regime and or cull the fish mass. This way i can always feed the maximum. So controlling/managing is done through testing and is always related to maximizing plant growth.