With that Kraken x40 you don't need it to be water cooling friendly. When NZXT (Kraken x40 and x60) and Corsair (h80i & h100i) were invented they were intended to be used on cases that didn't support water cooling. That being said you can use any case your heart desires as long as they follow this one rule for the Kraken x40.
The rear exhaust has to be a 140 mm fan, since the Kraken x40 will not fit a 120 mm fan. That being said the only reason you would need a case with water cooling or why they were invented for that matter was so people could build there custom loops and have them externally going into the case itself. The only thing you need is a rear exhaust fan for the kraken x40 that measures 140 mm (not 120 mm) since that will not work (the holes will not line up). That being said your Bitfenix Shinobi does not have a 140 mm fan, so it will not work. Here is a suggestion that would work with your setup:
PCPartPicker part list /
Price breakdown by merchant /
Benchmarks
Case: Rosewill CHALLENGER ATX Mid Tower Case ($39.99 @ Newegg)
Total: $39.99
(Prices include shipping, taxes, and discounts when available.)
(Generated by PCPartPicker 2013-09-29 03:07 EDT-0400)
That does not have the 140 mm fan on the back like we talked about, however it does have one on the top of the case (where you would mount your Kraken x40, and if it supports dual 140 mm fans on top, later you could mount the Kraken x60 for even better cooling. Hope this helps and please remember to select the best solution so that others may learn from this thread. Thank you for your time.