This is something I first noticed when I was at an aquarium in Japan (as evidenced in my examples) and continued to see ever since. There are certain pairs of animals, that while extremely similar, have certain distinguishing characteristics such that English speakers (well, most anyway) know them apart; or at least that they are different animals even if they don't know which is which.
Disclaimer - I'm no animal expert, so I may mix up these pairs, but I'll try to Google them to be sure.
For example, alligators and crocodiles. English speakers know these are different even if they're not sure what the differences are. Alligators have broader, rounder snouts, while crocodiles have longer, pointier snouts. Also something about the teeth. But in Japanese, they're both just ワニ. I asked my Japanese friend, and he said the average Japanese person doesn't know this difference or is even aware that they are considered different animals.
Here are several other pairs that seem to just get lumped together in the same Japanese word (by the average person):
- Turtle (flat wide shell) vs. Tortoise (large dome shell) → 亀【カメ】
- Seals (have fur; concave ears) vs. Sea Lions (smooth body; protruding ears) → アシカ
- Dolphin (have a "beak"; spiky teeth) vs. Porpoise (no beak; flat teeth) → イルカ
Even pairs that are blatantly different often get grouped:
- Crab vs. Lobster → カニ (not sure if Japanese people use ロブスター or not)
- Mouse vs. Rat → ネズミ
- Monkey vs. Ape → 猿【サル】
There are many other examples, but these are the only ones I can think of right now. I'm sure the 学名 are different, but like I said, it seems like the average Japanese person doesn't make, or even know of a difference in these pairs. Why is this?
Answer
First, I think speculating on what people actually know based on what options the language provides is too speculative. For example, I don't know the difference between a porpoise and a dolphin, even though the English language provides the option to specify either one. So the issue of what Japanese speakers know should simply be put aside.
However, it is worthwhile to consider why it is that Japanese, as a language, does not differentiate between certain animals.
Some examples you cite actually do common have common enough differentiations that I don't think they are representative of what you are asking about. ネズミ means mice and can be used for rats, but rats can be specified with ドブネズミ. Also, sea lions are アシカ and seals are アザラシ.
With the rest, you can notice a pattern. Japan has turtles, dolphins, and crabs. It does not have tortoises, porpoises, and lobsters. It shouldn't be that difficult to see how animals which were exposed to the culture relatively recently, and are so similar to known animals, that for the average person, they use a similar word.
However, note that although they are not common, and maybe mainly used in scientific circles, there are words for all animals. So tortoise is リクガメ, porpoise is ネズミイルカ, and lobster is ザリガニ. I have seenザリガニ offered in restaurants, though in the long run it might lose out to ロブスター. Wendy's in Japan, for example, offers a ロブスターバーガー (as of 2012).
With apes... you get into some interesting territory there. In my experience with English, "apes" usually refers to gorillas, chimpanzees, bonobos, and maybe orangutans (which wouldn't be quite right), but often does not include humans, unless the context is specifically about evolution or something similar where precision matters.
Even putting aside objections some might have about whether or not humans should be included when saying "apes", the scientific term "apes" actually includes two families of animal, one of which includes things like gibbons, which most English speakers almost certainly don't have in mind when using the term "ape".
So, the common English use of "ape" has some rather arbitrary lines drawn by culture, just as arbitrary as where Japanese draw the lines for 猿{さる}. Looked at that way, that Japanese doesn't differentiate between ape and monkey the way English does isn't a lack of specificity, but goes into other issues far beyond the scope of this question and answer.
Bottom line, though, is that in Japanese if you want to start talking about apes, you will have to be more specific than English: ゴリラ, チンパンジー, ボノボ, and, of course, 人間{にんげん}.
Just for comparison, Japan does make some differentiation not found in other languages as a result of the environment. For example, I believe it's because they have hot springs that they have the words 湯{ゆ} and 水{みず} for hot water and regular water.
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