Loaner words have definitely taken a big bite out of Japanese, but the tried-and-true original words are always around. Unless reference is being made to a concept that truly was not around in times before Western influence (like the television, or computer, etc.), there will always be an original phrase or word that was used first and may still be more polite or formal to use.
As far as understanding vocabulary with regards to more taboo (for lack of a better word) subjects, the solution for you is to go more scientific when you're searching for a word. There are absolutely words for using the restroom which may seem avoided simply because there is little reason to use them in daily conversation and they may cause discomfort.
I.e., imagine telling your friend very directly, "I am going to the bathroom to urinate." Most would rather say something vague like "I'm going to the restroom/the men's room/the ladies' room" or back in the day, the classic "I need to powder my nose." Some of us are more comfortable with directly expressing that we are going to "take a piss" or "have to pee" and the like, but in Japanese you will see that sort of directness in relation to vulgar topics only in the younger crowd or very, very close friends/siblings.
Curse words are of course very present, often the same as you can expect from the English language--vulgar references to people, excrement, and the like--and a few surprises that are perhaps a bit more ancient that involve corpses. But curse words are again more of the young in their use, or used in expressing solitary frustration. If you want to be rude, you might just go for a few subtle jabs by changing your conjugations. Or it's always fun to speak excessive keigo when you want to insult someone as it then comes off as sarcastic, "yes, your majesty"-esque. Honestly, rather than cursing at someone, it's more common to just speak more rudely to them, or just alter the way you say "you".
As for more sexual concepts, believe me the words are there. There will be more technical or scientific words, and there will be artistic innuendo-laced phrases that protect Japanese subtlety (usually involving sharing pillows), and there will be much more to-the-point verbs like penetration or whatnot.
Modern Japanese loves its loaner words but it also loves its subtlety and its tradition. The words are there if you get yourself a good dictionary and study up. I recommend the app "imiwa?" because it more than covers any and all of your questions about the versatility of the language and has a wide array of words and idioms spanning history.
