Kaepernick, speaking at his weekly news conference, called the reports "embarrassing" and pointed out disparities.
"I feel like anyone that believes that and goes about reporting that, just doesn't have the best integrity," Kaepernick said.
"To try to prey on athletes' livelihoods while one is going through a tough time is embarrassing to me. To put that out there and jump on that bandwagon just to get Internet clicks and get attention to their website, it really is embarrassing that people do that."
He said Smith was a good friend and that the defensive lineman attended functions hosted by Kaepernick.
"Yeah, I was good friends with Aldon," Kaepernick said. "He had just come to my camp, to my golf tournament for Camp Taylor this past June. He showed support and helped the kids out."
Smith was released by the 49ers on Friday, the day after he was arrested on suspicion of drunken driving.
"It's really tragic," Kaepernick said. "I wish him the best. I hope he's doing well. I hope everything turns out all right for him and he can get back on track. I know this team misses him and misses his presence here."
The 49ers travel to Houston for their first preseason game Saturday. Kaepernick will be introducing the team's up-tempo approach to the offense established by coordinator Geep Chryst.
"It took a little bit of time in the spring to get used to it," Kaepernick said. "At this point, I think everybody is comfortable with it. We've had a lot of time at it. And, it's something that Geep had talked to me about prior to, something that I've done in the past that he's done in the past. So, I think it helps simplify our offense."
Chryst hopes to steer clear of the huddle and allow his quarterbacks to figure out any issues.
"I'm really liking the way the quarterbacks have to solve problems in the huddle because we're on the sideline," Chryst said. "We're over here and we're trying to get the play in, so they've got to solve things because we don't have someone that can throw them a lifeline standing behind the huddle."
The faster pace has made for simpler play-calling, as in syllables instead of words.
"There's been a lot of attention about how we're trying to keep our meetings to maybe a 30-minute block of time, and then 10 minutes to reload," Chryst said. "We live in a more condensed, 140-character culture. So, I think at least my kids probably spell you, "u." So you try to take advantage of some of that."
NOTES: Chryst said playing time in Houston will be discussed following Thursday's practice. "I know we want to see Kap out there, but it's a fun preseason and having Blaine (Gabbert) in these games, it's going to be fun for him. I'll be really looking forward to him. Even though he's been around, I think he wants to show the strides that he's made," Chryst said. ... Joe Looney, who has been used in multiple positions along the offensive line, has been getting most of his reps at center this camp. "It helps a lot being at one position," he said. "You learn the plays and schemes better. I've moved along the line and it's about where the team needs me. Kap is always telling us 'tempo, tempo.' We want to get to the ball fast, see the defense and run our plays."