Although most of the restaurants in Japan offer desserts, it is not common for Japanese to eat desserts at the end of their meals. On the other hand, Japanese eat sweet dishes during the day, most common is around 15:00. For Japanese, 15:00 = snack or snack = 15:00.
However, restaurants usually include desserts for their courses. Traditional Japanese restaurants offer fruits or Japanese traditional sweet dishes. Then, contemporary style Japanese restaurants offer mixture of traditional Japanese and western style sweet dishes for the desserts.
Mixture means adding traditional typical Japanese ingredients to the dish. For example, warabimochi, bracken starch dumplings is flavored by sugar, kinako(roasted soy bean flour) and brown sugar syrup. However, it is too conservative or old fashion to offer for younger generation, restaurants add vanilla ice cream to the warabimochi.
Typical Japanese dessert eaten outside of Japan is Matcha(green tea) ice cream which is not so common in Japan. Then, other desserts like daifuku or dorayaki are also not available as desserts in Japan. Daifuku(rice cake filled with red bean paste) and dorayaki(red bean paste between the sponge style cakes) are usually eaten at home around 15:00.
By the way, ordering coffee or English tea together with dessert at restaurant(except restaurants which offer French, Italian or other non-Far East Asian cuisines) in Japan is very rare. Some restaurants do not even offer coffee or English tea. Therefore many Japanese go to cafes or other places after finishing their meals to enjoy coffee and dessert.