I’d like to save a bunch of links to webpages for some of my research, and I really just need the link, almost like a bookmark. But it seems like I have to add it as a .MHT, or PDF, or plaintext file, and it seems like Scrivener is just trying to do some weird, slow parsing. Is there anyway to just add bookmarks to my research tab for me to click back to the original webpage?
Yes. You are looking for the References feature, which is a function in the Inspector (click the blue ‘i’ button to toggle it, and then the bookshelf icon at the top of the Inspector, to access References).
References come in two flavours: a list for the whole project, and individual lists for each and every item (toggle them by clicking on the references header bar). They a bit of a hybrid tool: you can store links to files on your computer, anything that can be targeted on your computer as a link (as is common for e-mail programs), web URLs, e-mail addresses, and of course other items inside the project itself.
You’ll find more information on the References feature in the user manual PDF, §18.5, References, pg. 178. They are also introduced in the interactive tutorial, step 5d.