Speculation regarding the pair, which was rife throughout the summer, has re-emerged this week ahead of the opening of the winter window in the New Year.
Reports continue to link Hernandez – who could be involved in Monday’s game at Middlesbrough – with a move in January to Aston Villa where former Tigers chief Steve Bruce is in charge.
Boro are reportedly lining up a £6m bid for defender Maguire, having not been put off despite seeing two offers of £4m and £5m rebuffed in the summer.
But Phelan is adamant that the club’s major concern is bringing players in as he seeks to cover his bases across a weak-looking squad that has been hit by injury of late.
On the situation regarding Uruguayan international Hernandez, he said: “I do not see why he will not be a Hull City player after January. He is contracted to this football club. Yes, he probably had opportunities in the summer, but the player has never brought that to me.
“I am assuming he is okay with everything. I can’t deal with speculation, that can come from third parties, so there is no point me getting involved in that.
“He is our player and, so long as he is our player, he will perform for this football club.”
On the future of ex-Sheffield United centre-half Maguire, Phelan added: “We are not in a position to move players on.
“We are actually in a position to bring players in, hopefully to strengthen what we have got. We have to get those deals done and over the line if we possibly can.
“January is a horrible month, it always has been, no matter if you are one of the top clubs or one of the bottom clubs.
“They all have different strategies to put in place and sometimes that can be frustrating when we cannot do that.
“Hopefully, we will be in a position where we can attract. If we can do that, it gives us a little bit more ammunition.
“We do not want to make ourselves any weaker.”