Train from Prague to Tabor to Cesky Krumlov

yes you can stop off at tabor and it is well worth doing so,lovely little town and 3 hours is enough to see most of the town. just hang onto your ticket and show it again when asked to on the train. sorry I don't know about luggage storage.
This is an extract from my trip there in 2011.
Tuesday 17th May

We have a day trip to Tabor today. I had heard about this place on travel forums and found out that it was easy to get to from Prague, Andy had some DVD’s of European train travel and Tabor was featured in the Czech Republic one so we decide to go.

Return tickets cost 382kc for the two of us and we left from Hlavni at 9.16 am, the journey was fine until we reach Benesov where we have to transfer to a bus as there is some engineering work being done to the track, about 30 minutes on the bus took us to some place that shall forever remain nameless, a 2 horse town in the middle of nowhere, we re join the train and are in Tabor about 10 minutes later than scheduled.

Once in Tabor we walked to the main town it is a 15 minute or so walk but there are buses you can use, we enjoyed the walk and were delighted by the small town of Tabor, it has a warren of streets that are quite confusing, for many years this was an enclave of the Hussites in the Czech Republic and they basically rebuilt the town, I am not going to give a history lesson, you want info just google it.

The place is really nice with a town square some obvious town walls and a very nice little tower which gives great views over the town and of the surrounding countryside. There is also a medieval museum within the tower building which is very nice and informative, cost for both tower and museum was 80kc each.

We have lunch in the restaurant Modra Ruze, pork steaks with ham, potatoes and loads of veg. (150kc); it was very nice though I wasn’t so keen on the potatoes. this was washed down a Staropramen beer (22kc).

Fed and watered we headed to the town hall and to the Husite museum there, nice exhibits and some great dioramas of battles ,all a bit lost on me as I just could not really work out all the history.

We then took the tour of the underground vaults that start here, The Museum and vaults tour cost 100kc for both.

The tour was great fun, you have to wear a hard hat and even someone as short as me bumps their head, we joined a tour with about 40 school kids and their teachers, the tour was in Czech and we were the only 2 non Czechs on the tour, the guide very kindly came to us at each interesting bit and explained in basic English where we were so we could check on the English crib sheets we had been given ,very kind of her it was not in her remit to do that but she kindly gave us that info. The tour finishes in another part of the square and we return the short distance to the town hall to return our hard hats and crib sheets, it has been real fun. We then take a wander out of the old part of town and down to a waterfall area and carp farm, all very nice though the waterfall is a bit quiet, we then walked along the man made reservoir (there is history about why this was built, something to do with a fire in the old town and no water to put it out) back to the station.

It has been a great day, nice warm weather, a lovely town, a nice meal, and really nice people. This is a day trip I can recommend folk trying, not many English speaking tourists about, but a nice place with enough to keep you interested for the day and people that are genuinely pleased to see visitors.

https://www.cd.cz/stanice/tabor/5473622
done a bit of digging and it looks like there is a left luggage area in the train station in Tabor.

Thank you UncleGus for all the great information. We will be in Prague this May. I am looking forward to our trip.

you are welcome, have a great trip.