Hi Ferenein,
I don’t think you have anything to worry about with any of your concerns.
Latex layers (especially natural latex) usually have small imperfections and voids or areas of discoloration this is not something that is caused by bugs. It’s completely normal (see here)
The pincores in latex never go through the entire molded core. A latex mold has pincores in both the top and bottom of the mold so unless a layer is slit from a section of the original 6" molded core that only includes the top or bottom pincores the holes will only go part way through the latex. The depth of the holes will also depend on where the layer is cut from the original core.You can see some videos of how different types of molded latex is made in post #3 here. You can also see some pictures here of Latex cores which show the top and bottom pincores. The breathability of latex comes from the open cell structure of the latex.
I would need to have a closer look at the particles or feel them to be able to guess what they may be but they certainly don’t look like either bug droppings or molds or anything similar to me. Latex is very “sticky” and can easily pick up loose pieces of material or fiber from anything anything comes in contact with it and and they look like some type of crumbles from something that was against the latex. It’s also possible that they could be small particles of latex that come from slitting the latex. If they can easily be removed then it’s not something that would concern me.
I don’t see anything unusual or that would be concerning (even though I don’t know what the particles are) and hopefully this will put your mind at ease 
Phoenix