Why is that unsettling?
Let’s pretend you’re talking to a friend of yours, in English:
“Your kid still playing sports?”
“Yeah, seems we’re always buying stuff for it. Gonna go to the store today to buy him a new bat.”
Would you spend any conscious thought wondering whether he meant a bat, as in a wooden stick for hitting balls, or a bat as in a nighttime animal?
Maybe you work as a repairman and someone gives you a ring:
Hi, yeah I’d like someone to come out and help with some (leaks / leeks) in our master bathroom.
Would there be any ambiguity, would you be scratching your head wondering if they meant help with water dripping out of a pipe, or if they wanted help with a variety of onion?
There are a lot of homonyms in Japanese, and it might seem daunting at first, but when you realize you’re already dealing with these things automatically in English (or whatever someone’s native language might be) it’s just way less concerning.
As someone mentioned, certain words do have different pronunciation and pitch accent which helps you with the meaning. Perhaps analogous to record in English which could either be something like pressed vinyl for music (noun) or the act of taking the sound of music and transferring it to some permanent medium (verb) - these two words having different stress syllables.
Even without that though, if you asked a Japanese friend of yours what the weather forecast was, and they responded…
…you probably wouldn’t have to wonder whether they meant if it will rain, or weather candy will fall from the sky (even without the different pitch between them in standard Japanese).
Or likewise if you asked them what they did at the park today and they said…
…there probably wouldn’t be any ambiguity of whether they photographed beautiful flowers, or beautiful noses.
Unless your friend is really weird.