If you are on the Ostbahnhof platform when the train to Salzburg arrives, you shouldn't have a problem boarding, even with children. The conductor is standing on the platform watching and won't release the train while people are still getting on.
And boarding shouldn't be difficult. The last four times, at least, that I have taken this train it's been a modern double-deck RE, with the vestibules at platform level - just roll across the gap - no narrow, steep stairs where the kids might need help getting on with luggage.
As far as the neighborhood is concerned, I have never stayed around there overnight. The closest I came was just inside the "town walls" to the east of where your hotel is, but I have never felt unsafe in Munich at night.
That neighborhood is often described as a little "seedy". There might be a sex shop down the street, but nothing dangerous. Where you are staying, Cocoon, there is a place described as a "table dance strip club" 1/10 of a mile, around the corner and down the street from Cocoon, but it's away from the Hbf. You shouldn't encounter it getting there from the Hbf.
As for breakfast, I said on a another thread about breakfast near the Hbf, hotels have become infected by the airline disease of "unbundling", where they strip every conceivable service from the base price, making them hidden, with the base price very low, very low profit, and then add everything hidden back as extras at an outrageous price. Case in point, Cocoon wants 20€ for breakfast. That's too much even for an adult; I hope their child's price is lower. There are few restaurants around the area open for breakfast. The only place I see is Coffee Fellow, a German chain, which charges over 5€ for an avocado (or similar) bagel, but it might be less expensive than Cocoon. But Coffee Fellow is right next to that table dance strip club.
When I was last in Munich, we enjoyed breakfast at Woerners. There are two Woerners' "near" your hotel, one near Sendlinger Tor and one at Marienplatz. Both are over a km walk from your hotel.
