The Gunners duo will both be out of contract at the end of the season and neither player has penned a new deal.
Aside from the possibility of losing both players for nothing, Rooney has suggested that Arsenal should only be utilising players "who want to be there and you can put your trust in".
The former Manchester United striker told talkSPORT: "With the two of them not signing contracts in the summer, I think that told you everything. The way it is, I don't think they will be at Arsenal [next season].
"I feel they should have taken the money and looked elsewhere because, although they are top players and it is difficult to let those players leave the football club, when the going gets tough – as it is at the minute for Arsenal – you want players who want to be there and you can put your trust in.
"If they are not going to be there at the end of the season, maybe there are a few question marks."
Arsenal have reportedly braced themselves for the possibility of losing up to eight first-team players next summer.