Lens transmission does have an effect on brightness, but it's usually small compared to exit pupil effects. Most scopes have 6-11 lenses or other glass elements, such as an etched reticle. Typical multilayer anti-reflection coatings transmit about 99% per lens for green light, the color for which transmission is usually measured. Very expensive coatings transmit a little more (99.5%), cheaper single layer anti-reflection coatings less (97-97.5%). Most scopes above a $500 price point have fully multi-coated lenses.
With lens coatings, you tend to get what you pay for. Most scopes in the $300-600 price range will have a total transmission of 80-88% and 7 lenses or less. Scopes above about $600 range have fully multi coated optics but more lenses, so the total transmission rises only to 85-93%. A few companies are able to push the limits and get 95% transmission, but those products are usually in the $2,000+ range. There are exceptions, but they are uncommon.
So, the difference in transmission between a decent scope (88%) and a very good scope (95%) is only 7%. However if your eye pupil diameter is 6 mm in low light and you put a 50 mm scope set at 10X in front of it, the brightness will drop by 30% due to the pupil effect alone, which is a much bigger effect than differences in lens transmission from one scope to another in a similar price range. If you back off the magnification from 10X to 8X, however, the brightness of the 50 mm scope goes back up to that of the naked eye (less the loss due to lens transmission).
Can a person see a 7% difference in scope transmission in a side-by-side comparison? Probably, but it won't be dramatic. How about a 3% difference? Unlikely. I can't do it reliably and I've been working in the optics field for over 30 years. A 30% loss of brightness is pretty obvious.
To put it another way, if you set the magnification properly, the light loss through a decent to good scope will be about 10%, give or take a few. If you increase the magnification too far by only 25%, the loss in brightness will be ~40% or more.