Open second PDF file with hyperlink in first PDF file

The answer to your second question might lead you directly to a solution to the first.

You'll want a tool that edits PDF files to append docments (or conversely, split them up). I use PDFPen for the job, but there are others that do less but might meet your needs.

Here is an article on using Hazel to script PDFPen as well as documentation on how PDFPen is scriptable in general. There is a Pro version of the app for a higher cost, so you might see if you need the extra features, but the normal version seems to meet your needs well enough.

Many helpful PDFPen example scripts can be found after you install the software in your user library:

~/Library/Application Support/PDFpen/Scripts

Opening them in the AppleScript Editor is a great way to learn more.

Merged PDFs from Preview are perfectly valid and follow the standard. I've never found any incompatibilities with them. It does merge it into a single PDF, and any pages that are deleted are removed from the file. You can test this by checking file sizes first before merging, then after merging, then after deleting some pages.

The only drawback I've found with Preview is that the Apple code for writing PDFs seems to default to writing PDFs which are faster for Preview to render, but which are larger than typically put out by Acrobat. (At the moment, I can't find the link that originally proposed this hypothesis... It's been a number of years.) For example, you might open an Adobe-created PDF in Preview, immediately save it to another file, and notice that it has expanded. This change in file size does not change the image quality in any way.

In general, the change in file size is not too much of a deal. It's only in rare cases (such as 120MB scanned PDFs) that I worry about which app I use to create the PDF.