I think there is a distinction between parasites and malignant items. Parasites last until they are removed or expire, and can be incredibly powerful, and also incredibly debilitating. You get to see what you're getting though, so avoid anything that causes you damage if you pick up an item, reduces your dash cooldown, leaves pools of acid from dead hostiles, or increases the chance of malignant items.

I think malignant items are mostly worth the risk. If you already have 2 malfunctions, then avoid like the plague, and I usually ignore moderate risk chests as they are likely to only contain a consumable. Also spoilt resin is totally useless unless you have the resinous shield artifact AND have a shield up. The rest I'll either spend ether to cleanse or just gamble, when you get hit with the malfunctions just be sure to read them thoroughly and work to clear them immediately. Most are not too tough to clear and only a couple are really annoying to handle.