Hi Andrew I’m in Thessaloniki at the moment and here are the answers to your questions curtesy of my father, a retired railway employee of Thessaloniki station.
Firstly the entire network of Thessaloniki metro at the moment is wholly underground. Extensions are under construction but nothing will open imminently.
Regarding the railway museum, we visited today to ask on your behalf about opening hours and they said Monday to Friday 10:00-13:30 throughout the entire summer. If you cannot make it these times then by previous appointment they could open up on Saturday as well. Just call 0030 2310 559590. However as it is manned by volunteers maybe try to make it during the week so they don’t have to make special arrangements. The museum is for free but they kindly ask for a donation of €2 if you can afford it.
That’s the website of the museum:
https://sfsth.gr/. It’s in Greek but try to translate it.
Regarding photography, firstly you can visit the main passenger railway station. You can walk around the platforms and station to take photos, you don’t need a ticket. Apparently my father told me you can walk along the track number 8 on a dirt road all the way up to the signal box where the junction is and observe the trains it’s all open access. Past the signal box there is security and you cannot go.
There is also a freight station. Address is Paleou Stathmou 4 postcode 54627. For google maps put: Parodos Stathmou 4, Thessaloniki, Greece. It is about 4 kilometres from the museum and about 1 kilometre from the passenger station.
I have attached photos I took this morning of the freight station. As you can see it is open so I could walk in and take the pictures with my father. The notice on the door does say (in Greek) no entry because of overhead voltage danger of electrocution but my father says he can wander around at will as I proved by taking the pictures. So you could take a stroll and take some pictures unless challenged. The track is not electrified only the overheads. After all the prohibition note is in Greek only. There is not really another spot inside the city to take pictures. If you have the time you could try a beautiful picturesque heritage line in the village of Pelion near Volos. It is open Fridays, Saturdays, Sundays during July. The train is called “karvouniaris” (smudger). However it is about 230-250 kilometres from Thessaloniki. Here is the link for information and tickets it’s in Greek and English
http://www.hellenictrain.gr/en/mythical-route.
I hope all this helps, let me know if you need any more info.