Sometimes the collective noun gives you additional meaning or maybe some poetic beauty. But most of the time it doesn't really add much. Most people will understand the phrase "A flock of crows" completely and some people won't even know that they could say "a murder of crows". Then there's the connotation of the word "murder" which you may not even want.
One advantage to using the collective nouns is that the collective implies the type of animal, so if talking about lions and gazelles you could say "The gazelle was overtaken by the pride" and anyone who knows that lions are in a pride would understand what you are saying.
The situation is comparable to Chinese, where EVERY NOUN has a measure word. You don't say "two chopsticks", you say "two sticks of chopstick". In English we can say "two beers" but in Chinese you have to say "Two bottles of beer". However, there are lots of cases where a "proper" measure word can be replaced by a less proper one, or the generic measure word (ge 个). If you don't know the word for "small round thing" you can say "two ge marble" if you want two marbles. It's not 100% correct but people will understand and that's the important part.