To try and add a little to what Nermander and utnik said above, I would say that two useful tools to have when producing a long document would be:
1. Good Planning, and;
2. Good Workflow.
First, make sure you have your page size correct. This might sound a bit silly but, because Scribus uses absolute positioning, any changes to the size of the page later on will mean a boat-load of changes to every single page.
Then choose which font(s) you will be using. It's very important to get this sorted early on. I know Scribus lets you change text formatting easily but changes to the font can make huge differences to the text in the document. Do whatever testing/printing you need to do to make sure that the font(s) you decide on are right for the document you'll be creating. This includes making sure you have the correct variants for the job. For example, might you be needing italicised or bold text? Make sure you have them before continuing, otherwise you may have to change the font at a later stage and that will cause all kinds of problems.
Then design your master pages with guides while keeping the baseline grid in mind. Add whatever "furniture" you want to have - page numbers etc. - and check that text and images will be placed well in relation to them. Use the baseline grid offset to make sure that text frames can be placed on the page without having to make adjustments each time. Again, take the time to do lots of testing/printing to make sure that everything looks right. (You might find that you need to change the font(s) depending on how things go.) Making sure that you don't have to make lots of changes down the line will save you a lot of time later on.
Then create styles for all of the text you will need. It might be a dull process but it will save you a lot of time. Obviously if you've made the correct font choices early on then you shouldn't need to change anything but just being able to apply the style quickly is much better than direct formatting.
Once you have done all of that you should then have a good foundation on which to build your document. Take the time to do the planning right and you will do yourself a big favour.
To expand a little upon what has already been suggested, the editing of long texts is best done using a text editor with a good grammar/spell-checker. Get the text as you want it in the editor first, then import it into Scribus when it's ready and then apply the necessary formatting using styles. Then you can start applying typographical formatting - hyphenation/tracking/etc. - to get the text looking good. Once you have applied the formatting and got the text looking right you will be able to see how much space the text takes up and you can then add the images and other things in the appropriate places. You might need to make some small edits but these should only be for typographical purposes and not major content changes. This isn't as "fun" as just throwing stuff on the page and seeing how it looks but you will get a better document at the end of it.
Adding PDF annotations (hyperlink boxes) should be one of the last things you do because - as you have seen - they don't move with the text if the text changes. One tip for this would be to create a character style - based on the body text style - with a colour you won't be using for the finished document and apply that style to the text where you want links to be added. Once the text has been properly laid out and you're finally happy with it you can then look for the coloured text and add PDF annotations where needed. Once the annotations have been added, you can then change the colour of the style back to black - or whatever you're using - and no-one will see the join. (Don't use a different font/variant as this might move text around, just change the colour.)
All-in-all, while Scribus makes it very easy to move stuff around and make changes - and it's nice to be able to do so - there's no real alternative to good planning and doing things in the right order.
As for splitting documents up, I think the advice above is good and there is more scattered around the forum. Basically, it usually a choice of getting more memory and/or a faster machine or splitting the document. No-one but you can say which way you go on that. However, try doing the planning/workflow stuff first and you might not need to do anything else.