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.