This isn't an issue with PIC S3. Starfleet has always been bad about cyber security and technical design in general. I'm very confused why people are acting like this is new.

Random people regularly take over the ship. Wesley did it once with nothing more than a tape recording of Picard's voice. Consoles have been exploding and killing people for centuries. The technology to fix this issue exists now. The holodeck inherently fails deadly, such as absorbing all the participants if its merely powered off incorrectly. They regularly conduct dangerous tests next to the warp core that could destroy the entire ship. A good example of this is when they were investigating how the crew of an entire ship disappeared and beamed a sample of a plasma streamer into a container next to the warp core. It promptly and violently exploded. They had no way of knowing how strong the explosion would be, and it could've easily overwhelmed the forcefield and ruptured the warp core. Starfleet is often incompetent when it comes to basic safety and security designs with its technology. It's not a surprise they designed a system that allowed a bad actor to take over the fleet.

It should be pointed out the changelings are likely responsible for the flaws. They infiltrated Starfleet and worked on creating a means to bring down the Federation. Then there's the fact people were assimilated without their knowledge. The moment they were connected to the Collective, the Queen had all the information and access she needed to compromise the new fleet technology. No amount of security will fix a scenario where the people who designed the system are enslaved, and all their knowledge is freely accessible to the person trying to break into the system.