I have stayed in both. The Malmo Hilton is a short cab ride from the railway station. You can easily take the train from Malmo station to downtown Copenhagen. The same train stops at Copenhagen Airport.

The Hilton CPH is over the road from the airport station. CPH Hilton has a great location as it is walking distance to both the airport and the airport station.

For sheer convenience, I would use the CPH Hilton, especially if you get the top floor - great view over to Malmo and the airport, as well as a nice lounge. I did not get the time to use the Malmo lounge so cannot comment.

However, it sounds as if time is tight, so location would win over price in my judgement.

Enjoy downtown CPH - it is a great little city and it functions beautifully.