Midfielder Cook was a key performer for the Cherries last term but has been restricted to just 29 minutes of Premier League action so far this season.
The 21-year-old, who made his international debut in March and was on standby for Gareth Southgate's World Cup squad, showed glimpses of his undoubted ability during Tuesday's 3-2 Carabao Cup win over Blackburn.
Howe says Cook has been left out of his top-flight starting XI because of the team's impressive 5-2 friendly victory over French club Marseille and subsequent strong start to the season.
"Naturally, he wants to play, any player would say the same. I think if he turns around and says, 'I'm happy not to play', there's a problem," said Howe, whose side host Crystal Palace on Monday.
"He's been unfortunate because going way back to the Marseille game in pre-season, we played so well I didn't want to change the team from that day.
"And then we've had a really good start to the season, it's been difficult for him to get his opportunity in the Premier League.
"(The Blackburn game) I think is his best performance. I think MK Dons in the previous round, he was maybe over-trying but (on Tuesday) I thought he was very good and he was a key performer to why we played so well.
"I've got some tough calls to make for Crystal Palace."
Callum Wilson's injury-time header saw the Cherries scrape past their Sky Bet Championship opponents on Tuesday.
They appeared to be easing into the fourth round following an early strike from Junior Stanislas and Jordon Ibe's penalty, before Rovers levelled through Craig Conway's strike from distance and an Adam Armstrong spot-kick.
Stanislas was making his first start since suffering a serious knee injury at Watford in March and Howe was unsurprised by the forward's immediate impact.
"I think he'll be delighted with the goal, I think it'll cap off what's been a really impressive comeback from training into the game action," said Howe
"Typical Junior, technically he's excellent and he's come back in such physical frame at this moment that I wasn't surprised by his performance."
Blackburn boss Tony Mowbray, who was unconcerned with his team's cup exit, handed a debut to former England midfielder Jack Rodwell at the Vitality Stadium.
The 27-year-old, signed as a free agent following his release by Sunderland, was playing his first competitive game since September last year.
"You wouldn't have looked at him and thought he was way off the pace and he'll only get stronger," said Mowbray.
"And he has to then compete to try and get in our team because at the moment he won't get in our team, but somewhere along the line he has to make himself an option."
Rovers' biggest concern following the third-round loss will perhaps be the suspension for defender Derrick Williams following his late red card for a bizarre deliberate handball as Wilson threatened to break clear on goal.
"Derrick made a decision, it is what it is," added Mowbray.
"He slipped, he should have just rolled on top of the ball and made the boy boot him."