How will hydroponic farmers adapt? Where will they economically obtain the necessary nutrient solution additives? Are there practical techniques to extract these nutrients from traditional sources, like urine or manure? The aspiring Mars colonist or hydroponic homesteader will need to figure this out, or return to traditional "regenerative" farming practices which compost biological waste and return all used-up nutrients and their constituent elements to the soil.
And for someone like a Moon or Mars colonist, even regenerative farming isn't simple. Composting relies on bacteria to convert waste products like nitrogen-containing urea, whose nitrogen isn't bioavailable to plants, back into useful and bioavailable forms like ammonium. Keeping cultures of bacteria alive and healthy indefinitely will be essential to a colony's continued survival. Are there practical chemical processes to replace the function of these microbes, e.g. to convert urea to ammonia without urease enzymes? I don't know. Maybe someone with more knowledge can comment on this.
I hope this problem can be solved. Hydroponics has many benefits, from dramatically lowered water consumption vs. soil-based agriculture, to higher yields driven by precisely-managed nutrient ratios. Spacefaring farmers will appreciate the weight saved by leaving all that excess water and soil on Earth. It'd be a shame to abandon this technology simply because we couldn't pivot away from fossil fertilizers.