Could you check in your preferences that the number of comics to display on each page is not set to "0" ?

Seems like Ubooquity receives a cookie that was not generated by itself. 
Could you try to clear the cookies in your browser for Ubooquity's IP (the one you use to access your server) and check if the error is still there ?

It should not. I did a few tests, and something seems wrong. I'll investigate further.

Well, HTTPS will work in Aldiko, as long as you do not activate "user management" in Ubooquity.
Not very satisfying, all the more since Aldiko is a fine application. But there is nothing I can do on my side.

I'll try to do a few more tests with Challenger Comics Viewer in a few days, last time I checked it was working. I'll let you know what I find.

As for Comic Glass, there is no integration through OPDS. The way I use Comic Glass is through its integrated browser (this is in fact to be able to browse my comics by cover with Comic Glass that I started Ubooquity). You can point its internal browser to your server and set it as home page (all in Comic Glass). Not a very user friendly operation, but it's a one time one.

A legitimate request indeed. I'll add it to my list, but don't expect it soon, unfortunately.

Unfortunately Aldiko does not seem to support OPDS authentication.
Cf the results of my tests in this post.

This is an Aldiko problem, so you should report it to the Aldiko developper.
(if you do it and get an answer, I'd be interested in knowing it as well)