Kyoto is Japan's cultural capital, so you might expect to find more opportunities to experience incense there, but Tokyo has some interesting palces too - Juttoku, in a rather out-of-the-way corner of Shinjuku, offers the opportunity to make your own incense:
https://juttoku.jp/exp/

For stores that might be interesting to explore, you can search for 線香の店 or 香舗 in Google maps, although the former turns up stores that specifically focus on items for Buddhist altars. You'll find more Buddhist type places around Asakusa and more "fashion" oriented places in Ginza, for example.