For example the following recipe:

The recipe ID is displayed as this:

So what is the issue with the recipe id being too long? Are you actually using it for something? This is autogenerated, I can potentially cut it off, but it appears that mods are adding more data to the stack there and if I cut it off I can't guarantee that it's going to be unique and thus it may cause you not seeing recipes for some of the items. Or I will have to implement way more complicated logic to provide a unique id based on attributes that I would have to define for each recipe.

well I would still like to understand why it is important to you. If you just turn off advanced tooltips it's hidden then.

Please make it shorter somehow. I took this screenshot with GUI size 3x, the tooltip box cannot be fully shown with maximum GUI size.

Also these objects are displayed as their default hashCode value, which could change every time game restarted, causing bookmark recipe functionality of JEI being bugged

At least "woodtype" part should only display it's name ("birch" in this example) instead of lots of unnecessary SoundEvent Objects displayed by the default toString() method.

Ok, now the JEI bookmarking being broken that's a good reason to change this.
Not sure where you're getting the info that a hashcode is used there (unless JEI somehow generates it for the recipe), but I will take a look at making this more polished.
It's actually much more likely that some mod that's adding all those soundtypes (because those are not adding by SS) has changed more data on the items and because of that it no longer matches, but I definitely want that to be less fragile.

I didn't close this, but have updated how the recipe ids are formed a few days back, which makes them cleaner and not as long as this by far so this is now resolved.