What I did:
I copied the following link: Rabatte auf Abonnements | Stripe-Dokumentation. Then I pasted it in my note.
What happened:
A part of the link got stripped - an important part if I may add, so it was rendered like this: Rabatte auf Abonnements | Stripe-Dokumentation
What I expected:
I expected the full link to be rendered. Even though clicking on the rendered link does open the correct link - this is an issue since there are tons of modern websites (not to mention web apps) using the hashtag in their links so it would not be possible to differentiate between different links in the note.
I just installed the app and am on the last version of High Sierra.
We have opted to simplify links as much as possible. You can right click to go into edit mode and see the full link. You can also edit the text to something more meaningful.
Is your complaint that we strip the # argument? Or is the complaint that we modify the link appearance in any way at all? We might be able to keep the #, but in general, we are in favor of cleaning up long ungainly links.
Stripping the # argument can be a problem - we’re talking about a legitmate part of many web links. Also, I think you should consider the fact that there might be a number of (web) software developers using this system or anyone technical who’d like to see the full link when they paste it there.
Please read as this was said in a mellow, cooperative tone 
-> What you’re saying here is you made a choice to “clean up long ungainly links”. But they are ungainly from your perspective. Not everyone has an OCD-like need to format their notes like that. Personally I do these things myself (I’d rarely paste a raw link - I’d rather put the page title and link it myself - except in this case for example - where I was pasting something from someone else’s email).
That being said - you could offer an opt-out from that particular feature in settings.
Thanks for the follow up, I think we agree and have the same goal. We want to keep what’s important about a link (the anchor certainly is, we’ll fix that), but ditch what’s not (the scheme if it’s not something else than http or https, and parameters like those of google analytics). We also adapt based on feedback, for example the parameter is the only thing that discriminates youtube links, so there we do keep them. We’ll evolve and finetune the system as we go…
Update: The 2.0 update of Agenda should keep the anchor part of a URL when you paste links into a note.