Synthetic fertilisers aren't balanced to provide optimum nutrition in crops, unfortunately. They make crops grow well, but leave it depleted in many nutrients. Land is intensively farmed in conventional farming to produce high yields, less intensive organic farming generally creates soil with higher levels of nutrients. It's obviously not perfect, but it's better. I imagine manure contains more nutrients than synthetic fertiliser.
NHS doctors aren't trained in nutrition (or only have literally a few hours training) that's why they only recommend a few supplements like iron, vitamin d and b12 to address chronic deficiencies, not for optimal levels. Their speciality is drugs and surgery, whereas nutritionists have in-depth training in diet, and helping people get their nutrients up to optimum levels for good health, not the minimum needed to prevent diseases caused by severe deficiencies.
It probably is a good idea to get supplement levels checked for things like vitamin d and iron taken long term, if you can access a GP to request blood tests, or pay privately. Unfortunately in my area it's almost impossible now to even speak to a receptionist, never mind have a phone consultation with a GP. I wouldn't take more than 2000iu vitamin d (which is what I take in winter) without having an occasional blood test. That's much lower than the maximum of 4000iu advised by the NHS. I do my research from different sources before taking anything, take moderate rather than high doses and am especially careful with things like vitamin d that can be harmful in excess. Magnesium taken at 300mg daily is a safe dose, that's just below the RDA for women. Iron is best not supplemented if you're not deficient imo, but it's in most multivitamin/mineral supplements, which is probably shouldn't be. I feel much better for taking the supplements I take, so that's good enough for me. The NHS have nothing to offer people like me with M.E. I was fobbed off by GP's for years and had to go private to get an official diagnosis, I'd self diagnosed way before then. I've done loads of research, spent a fortune, and tried many things in an effort to find something that makes me feel somewhat better.