These are the descriptions I would use. As a general rule, you will want to try and use a description that is:
- Generalized enough that it encompasses everything you've listed
- Specific enough that it is clear what you mean. "Things" would be correct in most cases, but it doesn't particularly reveal what kind of things we are talking about.
- What about equipment and tools?
Equipment seems the most generic description available. Tools are a form of equipment.
- What about food, drinks and other beverages and fruit, vegetables?
Food can include both food and drinks, when used in the most general sense of the word.
- What about weaponry, suits, night-vision goggles, helmets, grenades and ammunition?
Materiel. This is an established term (most often used in military context, but according to Merriam Webster it is also correct in a corporate environment).
Medicine. If your question only lists a single type of item, then that is the correct name to use :)
- What about plants, flowers, different trees and other?
We tend to use flora, which comes from fauna and flora. Quite literally, it translates to "animals (fauna) and plants (flora)".
Plants would of course also be correct, but flora implies a more general biological definition.
- What about oxygen, hydrogen, different chemicals and substances?
Chemicals would be correct. However, people (wrongly) infer "chemicals" as "dangerous liquid compounds".
Substances would also be correct, but it is a bit vague. It also carries a connotation of being related to drugs. E.g. "substance abuse" inherently refers to alcohol and drugs.
I would use chemicals. In my opinion, we should not avoid using the word because some people wrongly infer a different meaning.
- What about living organisms and specimens and test subjects?
If you use flora for plants, I would use fauna for animals. However, if all of the cargo can be considered test subjects, I would refer to them as such. "Specimens" is too vague, because saliva swabs are also specimens but by no means an animal.
"Living organisms" can also include bacteria and microscopic life forms. "Fauna" can't (it is limited to animals).
If you mean animals, use fauna (or animals). If you specifically mean lab animals, call them test subjects (or lab animals).