Hebrew is just consonants??

Kinda, but not really.

The letters י ה and ו were later inserted into the text of Hebrew to represent certain long vowels to assist in reading. These are called the 'matres lectiones,' or 'mothers of reading.' When these letters were inserted, the scribes who inserted them weren't 100% consistent though, because there are often words where you would expect a matres lection, but one isn't there.

א doesn't necessarily, as far as I know, represent a vowel, but sometimes loses its consonantal value and lengthens the vowel that comes before it.

How much "later"? I don't believe that's accurate. It seems that the matres lectionis were included as part of the text, though inconsistently used, from the very beginning of Hebrew writing. You would have a hard time proving that this happened only "later" because it is everywhere in Hebrew writings, both biblical and otherwise, and from the earliest of times. Can you find a single piece of Hebrew writing from any period at all that doesn't have any vowel letters in it?

I mean, sure, we could find מאורות (me'orot) "lights" or מארות, but you will not find מארת with any regularity at all. And that is anywhere in Hebrew literature. The lack of vav in the feminine plural ending will never be found as "regular" at any point in Hebrew orthography.

aleph and ayin are vowels by any standard. heh, waw and yod may be vowels as well as consonants.

I disagree. Aleph and ayin are not vowels by any standard. Perhaps you do not pronounce these consonants, but they are consonants nonetheless. Aleph is a glottal stop (&#660 and ayin is a voiced pharyngeal fricative (&#661. The other three may represent vowels, as you stated.

The aleph does at times quiesce when it is not carrying a vowel, and in those times it is indeed silent. It is not until the time of the Dead Sea Scrolls that the aleph began to be used as a vowel letter in middle-weak verbs of the third-person singular perfect, as in קאם instead of קם ("he arose") and שאם instead of שם ("he put"). This is not a regular use of aleph in the biblical language. (We have the word כאן "here" of later origin in Hebrew, in which the aleph is a vowel letter.)