Usually english speakers are the candidates with the problems of homophones, because every unstressed syllable becomes a shwa.
To demonstrate: jeebus, jeebis, jeebes, jeebos and jeebas can all sound the same in English.
Other languages haven't the same problem.
But even in English you would probably say /painus/ and not /peenus/, wouldn't you?
For example in German "Penis" is pronounced with an /eh/ for the 'e' and an /ih/ for the 'i'.
And Pinus has a distinct /ih/ and /oo/ . Not an /ai/ for the 'i'.
In conclusion, it should sound distinct in many languages.