1) is this Intercity ticket available all year round and easy to get on the day of travel? Can we pay by credit card or cash? what is the currency?
Yes, all year round (but prices might change slightly from mid December - new timetable and maybe new fares). As far as I recall you can pay with credit card too. Slovakia uses Euro, but in case you pay with card it doesn't actually matter (your card will be charged with certain amount of money equal to sum in EUR with a help of the official currency exchange rate)
2) I plan to have a stopover at Melk and cruise to krems then train back to vienna. This involve a bus transfer since krems is not on the main train line. Do i need to purchase additional ticket for this transfer?
You can take a train for Vienna-Melk route only once (and Melk-Vienna as well once) with CityStar, so in case you plan go Vienna-Melk(train)-Krems-Vienna(bus)-Vienna-Salzburg(train) your Vienna-Melk part would be already used on your trip from Vienna to Salzburg (Melk is in the middle between Vienna and Salzburg) - means need to purchase new Vienna-Melk ticket+ after Melk use old CityStar ticket.
In order to avoid buying new ticket you either need to do Vienna-Melk-Krems-Vienna trip fully by bus or go as was said earlier Vienna-Melk-Krems-Melk(by bus)-Salzburg...