I would think plant life would usually supplant artificial systems for reasons of space efficiency. But as mentioned, it boosts morale by feeling more natural. Plus, mixed systems might include hidden or invisible parts, like algae growing in tanks that are fed light and waste water to produce oxygen and convert waste products into more useful things like food etc. Hydroponics, aeroponics, aquaponics and anthroponics are viable part of agro-industries already today. Mixing water, human waste products, water borne animal life, standard atmospheres and different gravity levels will become a major factor in space travelling in the near future.
For Traveller the question is just, how designers imagine TL10-15 ships to work. This is the realm of space magic really from our point of view. Either the decision is that these technologies are integrated into every design - visibly or invisibly - as part of standard life support systems, but below the level of Highguards proper 'biosphere' option, or the decision is that this is not the case, because it's to expensive relative to its efficiency. Either way, life support systems somehow work the way they do and the technology behind them is either purely artificial or a mix of technologies.