Magazines never drop out of the loot tables. When you find all of the magazines in a series, the bonus boost from Perks is reset to 0.
Each magazine has an equal chance of being found in a container that has them unless you perk into one of the perks. At that point, it adds a boost (usually from 20% to 100%) as you level up on the perks.
So if you perk once into living off the land, you have a 20% boost of finding seeds magazines. So using a Shamway crate as an example, you have two magazines in there - seeds and cooking. With no perks, you have an equal chance of getting either one of them. If you perk into LoTL at the first level, you have a 1.2/2.2 chance of picking the seeds one while only a 1/2.2 chance of picking the cooking one.
Also, I don't think you are getting hit as hard as some people think if you spread your perks around. A lot of the loot groups are setup to be specialized with magazines (so ranged weapons, melee weapons, etc.).
For example:
- 1 Perk in shotguns, cooking, armor, adv engineering, miner69er
- 3 Perks into knives, handguns, and bows
- So shotguns, cooking, armor, electrician, traps, workstations, harvest tools, and repair tools are 1.2
- Knives, handguns, and bows are 1.6
In a shotgun messiah crate, you would have (assuming one of the choices ends up being the crafting magazine):
- 27.6% chance of finding a handgun magazine
- 20.7% chance of finding a shotgun magazine
- 17.2% chance of finding the other 3 magazines (rifles, machine guns, explosives)
In a container that draws all magazines from, you have the following (assuming one of the choices ends up being the crafting magazine):
- Level 3 perks: 6.1%
- Level 1 perks: 4.5%
- No Perks: 3.8%
So putting points into the perks moves the chances a little better for that crafting magazine, but you are not getting penalized greatly doing so.
The second is that you should not waste points in Physician or Living of the Land. These two magazines can be found in abundance anyway, even without a boost. And if possible, you should only put points into a few perks that boost skill magazines. I try never to have more than 4 perks active at the same time.
If the only reason a person is putting points into those perks is to get magazines faster, than true.
However, there are other benefits from those perks to spend points into:
- LoTL - reduction in crafting costs for farm plots and increase harvest yields
- Physician - instant cures of sprains, faster crafting in chemistry stations
The magazine find is a bonus part of the perks, but should never be considered as the primary reason to perk into them. If that is the only reason you perk into those categories, then it will always seem to be a waste of a perk point.