ipadpassword
I know it is possible to save form username/passwords on the iPad's Safari browser. The thing I can't do is to save .htaccess username and passwords. In case you don't know what those are, it's when a webpage is protected and you can't even see the page without authenticating. It usually displays a popup window so you can authenticate.
Is it possible to save this type of credentials?
Yes. Go to the Settings app, and select safari. There will be a section called "Autofill", and you can enable it to save your passwords and auto-fill your personal information taken from the address book. Also, iOS automatically saves all Wi-Fi passwords, so there is no need to save it manually yourself.
You might want to exclude 'www' if possible. This can cause the page not being available as www mainly is pointing to port 80. If that doesn't work it might not be an Apple issue, and SuperUser might be a better place to ask the question.
Or you could set a redirect on a url pointing it to the right location with matching portnumber.
I can run different sites with portnumbers in it, as stated in the comments above. Example: Synology NAS port 5000, works on my iPad.
Best Answer
For a more secure solution, I'd suggest 1Password for iPad. It has many useful features, not the least of which are auto-generation of strong passwords (so you can use a different password on each site) and strong encryption of your passwords. You can use 1Password with HTTP Authentication.