Actually in Japanese the kanji makes it much easier to guess meanings, especially with place names which look bland and empty in romanji.

It's pronunciation that's hard to guess from kanji.

I like how there are two ways to say "I have a headache" in Japanese, and they are written with the exact same Chinese characters, but are pronounced completely differently:

頭が痛い (atama ga itai)

頭痛がする (zutsuu ga suru)

you think that's cute?

harakiri (腹切) is seppuku (切腹) backwards

Also in Chinese, "我有頭痛", tho "我有头疼" is often used in mainland speech.

"我有頭痛" sounds very Taiwanese. This usage of 有 is an artifact of Taiwanese / Minnan dialect. The Standard Mandarin （普通话） way to phrase that sentence is just "我头疼" or "我头很疼". Also like you said, 疼 sounds a little more mainland and 痛 sounds a little more Taiwanese. A general word for "pain" is 疼痛, they are really synonymous.

You can also guess Kanji readings just by looking at them. The largest class of Chinese characters consists of the "phonosemantic compounds", which consist of a phonetic part (how to say it) and a semantic part (what it means). Over 90% of Chinese characters fall in this class, but I'm not sure what rate you'd encounter them in Japanese. You can start doing this fairly well once you know... I'm not sure... probably in the vicinity of several hundred characters.

Several different readings is a bit of an exaggeration, it's more common to just have a kun'yomi and on'yomi reading, and on average I think the number of readings you'd know for a character is between one and two.

Purely from personal experience, I hear adult native English speakers (including myself) mispronounce words all the time! It's a common mistake to pronounce a word as if it were borrowed from e.g. French when it was really borrowed from Greek or Latin. So if you want to know how to pronounce "ch", you might say /ʃ/ if it's French and /tʃ/ if it's English. This seems to me like another variation on the same problem we have with reading Japanese, where characters have Japanese and Chinese readings.

You can guess the readings?

昨日 is sakujitsu or something? nope, it's kinou 明日 is just as bad

行く can be both iku and yuku, good luck telling them apart