Right now it seems that every zoo approached it differently, but not many announced that daily limit yet so we will know for sure probably next week. Brno announced their limit on cca 5 500 people. That would give us area of 36,6 ha, which is slightly over 50% of their reported area (65ha) so it is safe to assume they use the public space only method.
Jihlava announced the cap on 1 500 visitors daily which means they use, whole zoo area, but given the fact that Jihlava has basically non-existing off-shows, it is probably accurate for the public space as well.
I would say that for the most zoos the cap is most similar to the Saturday/Sunday level of attendance, rather than let's say middle of a working week, maybe a bit more than usual for some zoos. The only zoo I feel might be slightly handicapped by this is Jihlava, but only during weekends with nice weather.
If my math is correct, the daily cap of Prague should be around 9 000 which is perfectly fine for them at this time of year I guess. Also as reported, the director of Prague isn't happy with this earlier opening, so they might even set the cap lower.
No zoo announced such measure, Brno even said they were thinking about switching to off-season prices, but eventually decided not to, so they won't lose more money.
I am not an IT guy, so I have no idea what are the costs of such thing here. But most of the zoos didn't have an e-shop before, so now they have to rush it during the weekend. Some of the smaller ones even think about using e-shop of other company (as a sort of partnership) so they don't have to set it up themselves. Also as I said, the owners of these smaller zoos can't quite fathom why the tickets have to be sold online, but having souvenir shops open is perfectly fine...
Some zoos (Usti, Olomouc, Vyškov, possibly Plzen) already announced that their opening will be delayed to beginning of May so they can better prepare everything to be in accordance with government ruling and don't rush it.