{ghoj} and {ghojmoH} only count as one word because the second version
is only a suffixed version of the first.

Add {ghojmoHwI'} to that list.

But are you questioning the "one-wordness" of these words because learn, teach, and teacher are considered different words in English (and maybe German), or because of some inherent reason to do so in Klingon?

In English, we generally consider inflected forms to all be the same word, but not all affixes. Teach, teaches, taught, teaching are all the same word in different forms. But teacher, teachable, teacherly, teachability, unteach, and teacherage are all considered different words, not to mention words you can coin on the spot with suffixes like teacheresque, teacherlike, or teachaholic. And what about clitics, like teacher's?

So what makes you decide that -moH and -wI' have special standing to form new words? Because they appear in The Klingon Dictionary with their own entries? That wasn't done because they're considered separate words; that was only done to make English–Klingon lookups easier: a new student looking for the word teacher isn't going to look up the word learn and then add a -moH to it; they're going to look for the word teach.

What about -ghach? Is naDHa'ghach a distinctly different word than naD? naD is both a noun and a verb; the only thing the -ghach is doing is adding the -Ha' sense to the noun that already exists.

What about the type 2 suffixes? Isn't puvvIp afraid to fly a rather different concept than puv fly? Shouldn't it count as a separate word?

Let's not be so certain we know how to count words in Klingon. When confronted with the question, it would be much better to clarify that one is talking about the count of word roots, and that you can add many affixes to form longer words.

-- 
SuStel
http://trimboli.name