Take time to hang out in Deggendorf?

There is really no reason to buy tickets now, it is all regional trains to Munich, no reservations. From what I see, there is a train every hour at 45 past the hour. You connect in Plattling, 10 minutes from Deggendorf. If you hold off until 9:45, you can travel with a Bayern Ticket, 31 EUR for 2. That will save you from paying 63.20 EUR if you take the 7:45 or 8:45 trains. Added bonus, your Bayern Ticket will give you free public transportation in Munich until 3 am the next morning.
You could also take the 8:45 by buying a Bayern Ticket plus a separate ticket from Deggendorf to Plattling. I don't know off hand how much that is since it is a local district transit ticket. Can't be much for a 10 minute ride, 5 EUR maybe? The connecting train from Plattling to Munich departs at 9:02, so the Bayern Ticket will be valid on that one.

PS I should add that if the day happens to be a Saturday or a Sunday or a German public holiday, then there are no time restriction and you can use a Bayern ticket on the early morning trains.

Deggendorf is a pleasant enough town, but has no real big attractions The Handwerksmuseum has interesting exhibits if you are interested in crafts http://www.kulturviertel-deggendorf.de/index.php?id=509&no_cache=1&s=0CF9C0EF08A277AD93CEF8C9E1D08947811C83E1 and the alte Rathaus in the Stadtplatz is attractive. There are a couple of interesting places in the vicinity:
Schloss Egg - http://www.schloss-egg.de
In Niederaltaich, Gerhard Neumann Museum (inventor of the 1st jet engine to reach mach2) - http://www.f-104.de/english/neumann_english.html and also in a stunning Benedictine abbey - http://www.abtei-niederaltaich.de/php/?L=3
Personally, as you are taking the train to Munich, (change at Plattling), I would suggest you stop off at Landshut, a stunning medieval city. https://www.landshut-tourismus.bayern/de/stadterlebnis.html
Buy a Bayern ticket for the train, it also covers the buses in Landshut. You can buy the Bayern ticket on the day of travel. There is no benefit in buying in advance as the price is fixed, just remember to write the names of all passangers on the ticket to validate it. https://www.bahn.com/en/view/offers/regional/regional-day-tickets.shtml

Landshut is very enjoyable small town, so I can second "am Berg's" suggestion.

I will add that every year we try to include some town in our itinerary that is not a major tourist destination. We have enjoyed some of them so much that we have returned in subsequent years. We have never been seriously disappointed. I would not be afraid to give Deggendorf a try.

Deggendorf is a small country town. Typically for Lower Bavaria, it consists basically of a long square with the historical town hall in the middle and the baroque town church at the end. Enough for a one hour walk and a coffee. However, well worth seeing is the Baroque Benedictine Abbey Metten, which is 5 km away (impressive church, splendid library).

Lanshut sounds interesting. Is there a place in the train station we could leave our luggage or would we have to haul it with us?
Thanks for the feedback!

www.bahnhof.de shows luggage lockers at Landshut station.
Occasionally, we have stopped at towns where there were lockers at the station, but all the ones of the size we needed were taken. Then we hauled it to the Tourist Office and they were happy to hold it for us for a few hours. Your mileage may vary.
Landshut Hbf is about a mile from the interesting city center (and location of the tourist office), but they do have bus service. Use a Bayern Ticket, and the bus will be free. Just show your ticket to the bus driver.
PS Yes Bus 1 will take you from the station to Laendtorplatz in the old city.

You might consider spending the night in Landshut. If you do, we enjoyed two pretty decent restaurants: Augustiner an der St. Martins and the Hofbräuhaus. I like Munich but would prefer one less night there and spend the time Landshut.

https://mcchelsea.smugmug.com/Christmas-Markets-2009/Landshut-2009/i-RxL55tx

Thank you! I appreciate all the great info!