It's normal to find mostly ritual materials, especially in the earlier dungeons, but also later. You need those materials to perform rituals for more difficult chalices that you get from killing bosses.
The early dungeons have three layers and they end with the third boss. Later dungeons will have more extra rooms in each layer and up to five layers, so there will also be more treasures, but I guess "great loot" is rather subjective.
The main powerful items you can get from chalice dungeons are blood gems that can significantly improve your weapon damage, but the really good ones are gained in the more difficult dungeons as well. They are more powerful than any that can be found during the main game, and it is useful to search chalice dungeons for them if you want to maximise your weapon damage. In case you care what these blood gems can be like, I found a good farming guide on reddit that shows the effects of high level gems.
There is one weapon in the game that can only be found in a chalice dungeon: The Beast Claw. It is located in a treasure in the second layer of the Ailing Loran chalice dungeon.
You can also find upgrade materials in the dungeons. Blood Stone Chunks in Bloodborne are quite rare and it's difficult to farm them in the main game. In chalice dungeons, I had bosses drop them quite frequently with the latest game patch. In later dungeons there is also a chance to get Blood Rocks from beating bosses, while there is only one such stone per playthrough in the normal game.
Another advantage of doing chalice dungeons is that you will gain four insight per boss (I think two for entering the fight and two for beating the boss, but I'm not 100% sure about these numbers), which you can use to buy things from the messengers in the Hunter's Dream.
Still, treasures will often just contain more ritual materials to make new dungeons.
In case you care about Playstation trophies, there is also a gold trophy for beating the final chalice dungeon boss.
My personal opinion is that, in case you are still new to the game, chalice dungeons are not worth it yet. The difficulty of the dungeons increases quite abruptly as the depth increases and, as you noticed, the rewards are not really worth it. Chalice dungeons have a fixed difficulty and the later ones are even more difficult than the end game and are more suited for very high leveled characters (my character is level 160 and the late dungeons are still very challenging) or masochists.
However, chalice dungeons are a good way to prepare for NG+, because at that time you are powerful enough to beat higher depth dungeons and gain good blood gems and a lot of extra blood echoes.
To access the third ending in the game you need to consume 3 coords before the fight against Gehrman, The First Hunter, ends.
So anytime before Gehrman dies will still unlock the third ending.
Best Answer
No, you bring your Chalice dungeons with you to NG+'s. So you don't have to be afraid of losing them when you beat the game and go to a higher difficulty.