1. Any news about closures or bus replacement on my planned routes?
Well, there should be some minor changes in "Agram" schedule on HZ leg since 26/08, but it won't really effect your plans. With Zagreb to Rijeka & Split to Zagreb trains everything should be ok (at least we haven't heard about any problems with HZ domestic connections), same goes for Zagreb-Vienna EuroCity
2. Is it too risky if I have only 6 minutes to transfer from Sibenik-Perkovic local train to B 824 Split-Zagreb night train or should I travel back to Split earlier and board this train in Split?
Trains should be "connected", meaning that one will wait for another, basically this way HZ so to say attracts additional passengers
3. How much is a reservation in the sleeping car? How full is this train on a weekday(probably tuesday)?
Cheapest sleeper reservation (in case of train #824 it's T3) is rather expensive - 160 HRK. And since late August is kind of end of the season and many people going back from seaside, you can expect train to be rather full, so if you really want a sleeper reservation it will make sense to think about it first thing once you arrive to Croatia
4. Any experiences with the Rijeka-Split ferry? I'll travel deck class. Any tips how/where to get some sleep?
Few years ago traveled in early September on Dubrovnik-Split-Rijeka ferry (Split to Riejka was an overnight leg), everything went fine. Once it was still light just set on the deck on the back of the ship (it was Jadrolinija's "Marco Polo") and enjoyed the scenery. While at night some people just hanged hammocks and slept open air on the same deck, but I had a sleeping bag, so simply went inside and found a nice spot on the floor in a restaurant/cafe area (and many people did the same), so it shouldn't be a problem to get some night rest
Finally about fares, which I mostly figured out, but I'm not sure if it is right. Paying domestic fares a Zagreb - Rijeka + Split - Zagreb would be about 300 kuna which is about 40 EUR. Using the 60% discount for Hungary-Croatia return tickets it looks(according to jizdenka.cz) like a Nagykanizsa - Rijeka there Split - Gyékényes back return ticket costs about 40 EUR as well so iit's cheaper than buying domestic tickets.
Yep, if you don't have any discounts (like ISIC which works for HZ domestic tickets), then two tickets (Zagreb - Rijeka + Split/Sibenik/Perkovic - Zagreb) add up to about 300 HRK. Regarding trick with international return ticket MAV-HZ, in your case it might not work the way you want, because really doubt that MAV ticket counter easily will sell you ticket with Rijeka as final destination there, while Split as start for the outward journey. If you have time you can stop by the MAV counter and ask, but my guess, maximum you can get from them is ticket for the common part (till Oštarije)
For Zagreb - Wiener Neustadt(eventually Sopron) SCIC-NRT fare with Railplus discount would be about 50 EUR. Any chance to make this cheaper? I know about 29 EUR Sparschiene, but I can't book it online.
Yes, you can't purchase discounted tickets from Croatia online, but with Sopron factor first thing that comes in mind as a solution - visit to OeBB ticket counter and purchasing of the discounted ticket for EC 158 there, OeBB definitely can sell it. Other option might be to get in advance online discounted SparSchiene Österreich ticket from Spielfeld-Straß (easily purchasable via OeBB website, starts from 14 euro), while in Zagreb just purchase additional international ticket Zagreb-Spielfeld-Straß, with RailPlus it should be less than 25 euro