The answer is it depends.
What policy have you got set for mismatches? What do you want to happen? There's a LOT of complex interactions that can happen here.
First off, I'd continue to work with templates that have the correct workspace assignments. You can set the defaults in Bridge for the side that has the higher volume of work, and just assign the other space in ID when you need to.
Also to some extent it matters what sort of conversions, or non-conversions, you can handle and the type of vector work it is. For a lot of logo work that uses 100% K elements I save without the embedded profile in Illustrator. That guarantees that the imported art will always be treated as if it is in the current working space in ID so I don't get K -> 4-color conversions in the logos, but it also means that there can be color shifts if there are CMYK objects involved, too. I do this so I can use a policy that preserves the embedded profiles so that photos don't get shifted. You might be OK, too, with a policy that preserves CMYK numbers and converts to the current working space, but preserves RGB profiles as long as your photos are placed as RGB or are converted to the correct CMYK space before placing.
If you tell us some more about the workflow and files you'll probably get a lot of better answers and advice.
Thank you for the reply.
My workflow is literally 50% internal newsprint work (ISOnewspaper26v4) and 50% glossy magazine work (ISO Coated V2 Fogra 39)
PS for photos
AI for vector work
ID for layout
All PS, AI and ID work is CMYK (strict – neither our press or any external printer would accept RGB ID or outputted PDF files or any images / artwork within ID or outputted PDF files)
All AI vector work is strictly vector work and all black would be K plate only. Most vector art we use is from Thinkstock - I always transfer art to a new CMYK AI doc then I personally go through all colours with the white arrow, click on one piece, select similar, check the CMYK values, lock that piece down and move on to another piece until everything has been locked.
No spot or pantone, just pure CMYK. Black is always K plate only.
Essentially my question is this. If I set all my AI vector files as 'Assign Profile / Don't colour manage this document', will it affect how the artwork will look and / or output to pdf when it's brought into ID?
The AI files will still be on CMYK templates, they just won't have any colour management.
First, I wasn't suggesting that your PDFs be exported to RGB, but it is a common workflow these days to keep photos in RGB until you convert them to the correct profile during the export process. This maximizes the potential for re-purposing your documents and allows you to use the same RGB photos for different output purposes without having to do separate CMYK conversions for each destination, so long as you don't need to do any tweaking after the conversion.
And to answer your question, if the .ai files have no embedded color profile they will ALWAYS be considered to use whatever the CMYK working space is in your ID file, so the numbers will be preserved. This means that there will be slight differences in color on output on different devices (the whole point of color management, after all, is to preserve the appearance of colors by altering the numbers for the output device).
Does the vector work you get from Thinstock come with an embedded profile? Is there any color that is critical for matching, such as a corporate color (which should be spot, but that's a different discussion), or do you use the same art in both the newspaper and magazine, and does the client expect a match (which we know isn't going to happen anyway)?
If there's no embedded profile when you start, there's no way to know what the color was supposed to look like, so color management is not possible, really. You can assign a profile, but you'd be guessing. Since the correct appearance at that point is unknown continuing with out color management shouldn't present a problem. The only case where you would need to manage the vector art would be if the color APPEARANCE is critical or you need it to match across different outputs, and in that case you would need to assign a profile and allow ID to preserve the profile on import and remap the numbers, which means you would likely get rich blacks someplace. Since it's unlikely that you can get a good match going from glossy to newsprint, I probably wouldn't even try -- you wouldn't want, for example, to tag the art as newsprint, and have it print subdued on the gloss if it would look better or more correct with the other profile. Color management would be much more useful if you were going from sheetfed to web on the same stock.