By not saying anything they are loudly proclaiming that they have nothing to say about it and that they don't view Jontron's view as something worthy of being denouncing.
Basically they either agree with his views or don't find it offensive enough to come out against it.
Inaction is also an action.
If you do not denounce something people find vile it's clear where you stand and your silence speaks volume.
I disagree, and I don't think there's any onus on them. You're not guilty by association because you worked with someone that everyone thought was fine at the time, and then choose not to engage with the issue when it comes up later. If this came up 2 years after the game had already come out, my thought wouldn't be, "Hey, they released a game 2 years ago with JonTron in it, they probably support what he says because they haven't denounced it." I feel the same way now even if the game hasn't released yet.
As far as I'm concerned, JonTron has obviously outed himself as a racist, and the status of the Hat in Time devs is that they unknowingly worked with a racist. That's it. There's no shitty until proven innocent. It's just unknown what they think*, same as it would've been if none of this had happened in the first place.
*Although they apparently posted anti-Trump stuff on their Twitter according to some other poster.
Releasing a game being hard is not an excuse to be complicit in his beliefs. Sorry. It sucks for them but shit happens and you need to be prepared to not compromise who you are as a person to make things easier on yourself.
In no way does working with someone that was unknowingly a racist and then not offering comment when the world finds out they were a racist make someone complicit in that person's beliefs, lol. Obviously people are free to make whatever inferences they want if it makes them feel suspicious of the whole thing, but you're making it sound like there is implicit support unless there's explicit disapproval. I don't agree with that.