Hi Ciaran,
Went through exactly the same choice process about two months ago.
I actually already had a Ninja 100 cell sports cat from Scoobyworld which I bought new a few years ago for my WRX SL Blob, only I never got round to fitting it and mapping.
Initially my plan was to use it for the hawk, but I was concerned I might not pass NCT on the 2.5L STI with only 100 cell cat.
In the end I bought the Cobra 200 cell cat and if you look in
https://isdc.ie/forum/threads/27776/ page 45 about half way... I passed emissions with flying colours.
The welds on the Ninja were a bit nicer I think than the ones on the Cobra, but the Cobra does give a life-time-guarantee, even if you wrap it!
Note that Miltek, Cobb, RCM all replied that warranty is void if you wrap the exhaust (have emails I can dig out if you want).
Some, like Miltek, also lock you into having to buy other sections from them due to odd bore sizes and longer / shorter pipes, which will only mate up to their next section.
Cobra were very responsive with questions and advice so would certainly recommend Cobra from that point of view too.
BTW - apart from the Cobra down-pipe with 200 cell sports cat and TP48 back box from Cobra, I am running a H&S centre pipe with resonator. I previously had a H&S full system on my v3 and was happy with that, but the experience with the centre pipe from them this time round was not great. Welds not as good as before and the pipe was was cut and welded wrong so didn't fit (not with oem or cobra stuff). Ended up having to get it cut, bend, and rewelded by a local shop and nearly caused me to miss my mapping slot with Bob if it wasn't for Seanie swapping slots with me (THANKS AGAIN Seanie!). Hence I would now leave H&S. They also void warranty if wrapped and their work is not as good as it used to be.
Given all... quality, warranty, emissions and of course price... I would go for (full) Cobra again.
Ninja was very well put together with best welds of the three brands I compared side by side... just that 100 cell on 2.5 was chancing arm at NCT time and didn't want hassle of having to fit original cat for every NCT. If you have a 2.0L it should be fine (that's what Scoobyworld said to me when I bought it for my 2.0L) and if you're interested would do you a good price as no need for it now and was never used
