Naruto might use his shadow clones to do the brewing while he is off doing normal ninja things. That way, no one suspects that he is the actual brewer. Also, he could use his transformation jutsu to disguise the brewing equipment as something else when someone is around.
He could brew at a secret location, like a hidden cave or an abandoned house on the outskirts of the village.
To keep his brewing a secret, Naruto could use his skills in stealth. He would only brew at night when everyone is asleep. He could also cover up the smell of his brews with some other strong scents. And when transporting his brewing ingredients or finished products, he could use his ninja tools to hide them, like using a scroll to store everything so it looks like he's just carrying a normal scroll.
Well, perhaps in this fanfiction, Naruto discovers his talent for brewing by accident. He might start by brewing simple herbal teas at first, but as he gets more into it, he begins to create complex concoctions. His brewing could be related to his chakra control, like he discovers a way to infuse chakra into his brews for extra effects. He'd have to keep it secret because it's a new and untested ability in the ninja world.
Perhaps Naruto has developed a special chakra - based concealment technique. This technique would not only hide his physical identity but also any chakra signatures or auras associated with the Hokage position. He might use it when he is out and about in the village, so that even the most perceptive ninja wouldn't suspect that he is the Hokage.
Naruto could use clothing to her advantage. Wearing baggy and androgynous ninja outfits would help to conceal her feminine body shape. For example, the standard orange jumpsuit she often wears doesn't really give away her gender easily.
To keep their marriage a secret, they would have had to be very careful. They could have met in secluded places like an abandoned forest or a hidden cave. When communicating with others, they would be extra cautious not to let any hints slip. Natsu might have pretended to be just a friend to Yukino when around others, and Yukino would do the same. They might also have had a secret code or signal to let each other know when it was safe to be together.
She probably uses magic. For example, she could use a spell to mute any sound coming from her music player when someone gets too close. Or she might have a charmed diary where she writes about her love for the singer and it can only be opened by her magic signature, so no one else can find out.
In fanfiction, Naruto might keep the Rinnegan a secret by avoiding using its powers in public. He could also use his shadow clones to create distractions when he feels like the Rinnegan is about to be revealed. Plus, he could tell only a very few trusted people, like Kakashi or Iruka, and ask them to keep it a secret for him.
They might create false stories or alibis. Say if they go on a date, they would tell their friends they are doing something else separately. Also, they could be careful about leaving any evidence of their relationship, like not leaving love notes where their friends could find them.
They might be afraid of how their families will react. The Weasleys have their own ideas about who Fred should be with, and Hermione's parents, while muggles, might not understand a hasty and secret marriage. Also, there could be threats from dark forces. If the wrong people find out about their union, it could put them in danger, so secrecy is key.
It can add a layer of mystery. For instance, other characters might start to notice strange behavior from Naruto and Sasuke, like them disappearing at the same time. This can lead to various sub - plots where other characters try to figure out what they are up to.
In a Naruto becomes a weapon master fanfiction, he might achieve it through intense training. Maybe he meets a master who teaches him unique weapon skills. For example, he could learn swordsmanship from a hermit in the forest. This new knowledge would add to his combat abilities, making him a weapon master.