Webber will be 36 this year and there is speculation that the Australian might make way at the end of the season, even though he goes into Sunday's season-opening race here with all the confidence that made him a title contender in 2010.
Hamilton's contract with McLaren expires this year and he was so excited by the prospect of driving for Red Bull that he sought out Horner for impromptu talks in Montreal last year.
But Horner says he would prefer to look to Daniel Ricciardo or Jean-Eric Vergne, who make their debuts for Red Bull's feeder team Toro Rosso in this weekend's Australian Grand Prix.
Horner says: "I think that it's difficult to envisage Lewis in our team. I think he's comfortable in the environment he is in and we're certainly comfortable with the two drivers we have.
"We also took a decision to invest in youth and we have two really exciting youngsters entering GP racing in Jean-Eric and Daniel – both really talented drivers, and both deserve that opportunity. It will be fascinating to see how they evolve over the year. So we're more likely to look inwardly than outwardly."
Vergne will be making his F1 debut on Sunday. The nearest he has come to a race is totting up the miles on the team's simulator in Milton Keynes. The Australian Ricciardo entered F1 halfway through last season, when he drove for HRT.
Horner's comments are a reminder to Hamilton that his ambitions to add to his solitary championship, won in 2008, rest with McLaren; a move to Ferrari would surely be frowned upon by his old McLaren adversary Fernando Alonso and Mercedes does not have the car.
Many in F1 are wary of the baggage that Hamilton brings with him and Horner added: "It is important to have the right balance within any team, not just with the drivers but throughout the organisation.
"Whether or not it could work [with Lewis], who knows? Our preference would probably be to go with drivers in whom we have invested from a young age, give them the opportunity and see how they evolve rather than take something external.
"Lewis obviously had a difficult year last year – got involved in a lot of incidents. I'm sure he will be focused on trying to avoid that and that he will have learned from that.
"When Lewis came into the sport he was so strong, so quick. And then he had some tough experiences, which I'm sure he'll only learn from.
"So much depends as well on the equipment you are dealing with. He still has time in his career to achieve great things but that is also down to him."
But there may be no vacancy at Red Bull at the end of the season, because Horner has been impressed by Webber's pre-season form.
Australia has learned not to expect too much from the driver in his home grand prix. Sunday's race, which opens the F1 season, will be his 12th and his best result was the fifth he managed on his first appearance on the street circuit, driving a Minardi back in 2002.
But while his team-mate at Red Bull, the double world champion Sebastian Vettel, remains the favourite to win again Horner is convinced that Webber can be a real threat. "He is motivated, he is hungry, he sees a future," he said.
Webber won only one race to Vettel's 11 last season and struggled to come to terms with the Pirelli tyres. But Horner says: "I think the tonic of winning the last race of last year set his winter up very well.
"He's gone away, he's trained hard, he's come back lighter – he's lost about a kilo – and fitter than he's ever been, and he's more relaxed, noticeably so, within the team than he was 12 months ago.
"As he's admitted, the hangover of not winning at the end of 2010 carried into 2011, and at times last year it didn't look as though he was enjoying going racing. But I think he's got back his enthusiasm and his passion for the sport. For us, it doesn't matter which one wins it as long as one of them does."
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image: © David Wall