Honduras was the place I was told to skip, unless you wanted to scuba in Roatan
There were other backpackers in the hostels.
Even Colombia at that time was fine.
As the marketing for tourism Colombia goes “the only danger is you’ll never want to leave”
I wouldn't let fears of crime discourage anyone from visiting Latin America but compared to many other parts of the world you need to be much more aware of what's going on around you.
How did you cross that part of Colombia that is impassable and has no road and blah blah blah ?
Genuinely curious as I was dissuaded from a similar trip by the supposed inability to go all the way through Columbia.
I've read a number of articles about the Darién Gap, and they all indicate that there have been several ferry operators in the past, in some cases for years at a time, but that there's currently no regularly scheduled service. For example, Wikipedia states this several times
https://en.wikipedia.org/wiki/Dari%C3%A9n_Gap
Wikivoyage suggests that you can make it by boat if you're willing to fly part of the way, and/or that you can make private arrangements with a shipping company that can transport cars.
https://en.wikivoyage.org/wiki/Darien_Gap
My understanding from these and other articles is that people with enough money can buy access to sea transportation for themselves and/or their cars, but that you can no longer just buy a ticket for any kind of regularly scheduled departure. But this could conceivably change again in the future.