Yes, but just because you can do it better now doesn't mean the damage you inflicted goes away. If damage to frequently utilized space lanes leads to other ships that use them having rougher ride/accidents, for instance. Space pot holes. Or organisms that live in space can't feed/live as they once did because their habitat is destroyed.
Cumulative damage in the body can usually be repaired and is technically detected.
If regular transporters caused it, it would have been long detected by now (its the subspace transporters that do this, but you can still use it several times before suffering any permanent damage) .... but instead, Humans live on average 150 odd years in Trek (but oddly enough nothing in terms of biological immortality despite the fact they have the means to make it happen).
Warp drive causing issues was fixed.
Since UFP is a type of society where money doesn't exist... technology isn't made with cost efficiency in mind, but with technical efficiency in mind.
As such, any technology made for long term use would certainly undergo a ton of testing and inspections to make sure its not harming anyone.
Its other species who don't necessarily pay that much attention to the health and safety of their own people.
The Klingons would probably fail regular health and safety inspections as is.
Romulans and Cardassians... they'd probably be similar to Starfleet in this regard... maybe Caradassians more than the Romulans (the Tal Shiar probably wouldn't care about the regular military, but would otherwise care about the wellbeing of their own operatives).
The Malon on the other hand... now there's an example of a species that doesn't care.
The entire introductionary episode of the Malon in Season 5 of VOY went through the details on how a Federation ship recycles EVERYTHING (waste energy and theta radiation which is re-used inside the ship - so technically speaking, a typical UFP vessel or technology would really not emit any waste as all of it would be recaptured and used).
So, yeah... I'd say when it comes to UFP technology it seems rather safe... you can use it however much you like and won't be affected (unless you work in a dangerous area such as engineering and could be exposed to dangerous/but still accidental radiation or breaches that will land you in sickbay during attacks [even then it doesn't occur that much], but otherwise, not during regular operations).