The atmosphere in Nullius has a lot of carbon dioxide, much more than modern Earth. A bit like primordial Earth before photosynthetic organisms replaced the CO2 with Oxygen, or any number of other lifeless exoplanets. Over the course of the playthrough you'll need to consume a lot of it, and you'll naturally remove more from the atmosphere than you add. The plants you plant in the endgame will remove a lot more. Most of your CO2 will ultimately come from air anyway, so it's just returning it from whence it came (though some of it comes from limestone). So if you need to vent some here and there, it's not a big deal. If you have a process that is consistently producing a significant quantity of it, it may be worth trying to send it back and make use of it so you can reduce your air separation facility a bit. But if it's only a small trickle of CO2, it may be easier to just vent.
Some ventable gases list an oxygen reduction stat in their description, which may be a clue that it's better not to vent it if possible (carbon dioxide isn't one of these, but carbon monoxide is). All of your oxygen venting is being tracked, though you won't have visibility into that until end game. And with the exponential growth in manufacturing capacity, your early game choices are a drop in the bucket for total venting anyway.
Dumping some wastewater in the early to mid game is probably unavoidable, though your factory is still small enough at that point that the environment will be OK. Mid to late game it's possible to do stuff with wastewater and sludge, so if you feel bad about it you can try to minimize your waste by reprocessing it.
Caustic solution is not a big deal and dumping some may actually help. The oceans in Nullius have a naturally somewhat lower than ideal pH. One of the concerns with acid is that it's corrosive to your own delicate factory equipment, but caustic is much less harmful to your machinery. In real life it's acceptable in most jurisdictions to flush aqueous sodium hydroxide down the drain, as long as it's reasonably dilute. It's used as drain cleaner to clean the plumbing. Not only that, but food grade sodium hydroxide solution is actually a culinary ingredient that people add to food and consume. It may be used to treat our tap water supply in some places.
