Fronting the media on Monday, Hayes was the first St Kilda official to comment after Tom Silvagni was found guilty of rape late last year and jailed for six years.
Jack and Tom are sons of Stephen, who is a key member of St Kilda's list management team.
Jack joined the Saints from Carlton at the end of last season to bolster their defence, one of several high-profile recruits to Moorabbin in late 2025.
"We support all of our people. It's obviously been a really challenging time for their family," Hayes said of the Silvagnis.
"But we fully support Jack and Stephen. They're fully committed to their roles this year, as we are to them."
Jack Silvagni is recovering from a groin problem and Hayes said he was making good progress.
"He's on track today, so he should be back in full training by the end of the month," Hayes said.
"He's a quality player, but the leadership we think he can bring to our backline is going to be really pivotal."
Hayes, one of St Kilda's greatest players, returned to the club in 2022 as an assistant coach and will now run its football department.
"From my end, I had to be the right fit for the role ... to be able to take the club forward," Hayes said.
"After some discussions, we got to a point where we were really confident in the structure, that we could make an impact in this role."
Hayes was asked about being football department boss with Ross Lyon as coach.
"We can complement each other. We've been to some places that grown men sometimes shouldn't go to together," Hayes said.
"We've been through some good times together, we've also been through some really hard times together.
"We have a deep, mutual respect. I'm really confident we can work together on this and take the place forward.
"We'll work really well - hand in glove, if you like. There will be some challenging times, but I know because we have that respect, we'll be able to work through those really well."
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