Skill-points are very limited in Etrian Odyssey and I have to think hard, in which skills I should invest. Chop, Mine and Take have no influence on fights, but they can provide some material, that I don't get in another way (at least on the same level). How much should I invest in these skills?
Assuming you mean Etrian Odyssey 1, the best option you have is to build out a party of 3-5 Survivalists. Level them up a bit, either by themselves or with some members of your main party. They should work on Chop, Mine, and Take - Survivalists, unlike other classes, can learn all three - as well as at least one with Stalker and Escape.
Stalker lets you get to gathering points without so many encounters. Escape lets you get out of the few encounters you'll have. If you have more points, 1st Turn lets you Escape before the enemy even gets to go, even if their agility outclasses yours. Once you're done gathering, Warp Wire back.
Don't give anyone else gathering skills. You're right; it's a waste of points.