Suffixes that are words: why aren't they considered compounds?

Your wondering at this is understandable. In a very interesting article, which I recommend you to read entirely, M-W includes in the category of compounds the words formed with the help of prefixes and suffixes:

A compound is a word or word group that consists of two or more parts that work together as a unit to express a specific concept. Examples are double-check, cost-effective, around-the-clock, hand-to-hand, forward-thinking, eyeliner, and iced tea. They might also be formed from prefixes or suffixes, as in ex-president, supermicro, presorted, shirtless, or unforgivable.

It is interesting to look at the etymology of these suffixes. Take -wise for example. Etymonline explains that it comes from the NOUN wise (which is still used today in formal or literary expression like in this wise):

wise (n.) - "way of proceeding, manner," Old English wise "way, fashion, custom, habit, manner; condition, state, circumstance," from Proto-Germanic *wison "appearance, form, manner". Most common in English now as a word-forming element (as in likewise, clockwise); the adverbial -wise has been used thus since Old English.

So in modern English it is considered a suffix when it forms adverbs like timewise, moneywise, contrariwise.

As for -able (sometimes -ible), this is definitely a suffix, but is associated with the adjective able because of the similarity in meaning. Etymonline is again of great help:

-able: common termination and word-forming element of English adjectives (typically based on verbs) and generally adding a notion of "capable of; allowed; worthy of; requiring; to be ______ed," sometimes "full of, causing," from French -able and directly from Latin -abilis. It is properly -ble, from Latin -bilis (the vowel being generally from the stem ending of the verb being suffixed).

In Latin, -abilis and -ibilis depended on the inflectional vowel of the verb. Hence the variant form -ible in Old French, Spanish, English. In English, -able tends to be used with native (and other non-Latin) words, -ible with words of obvious Latin origin (but there are exceptions). The Latin suffix is not etymologically connected with able, but it long has been popularly associated with it, and this probably has contributed to its vigor as a living suffix.

So if you check the etymology of these suffixes, you will elucidate why they are only considered as word-forming elements, and not words in themselves.