say, for example, the RN decide that we need to replace the CIWS onboard a ship with a newer model... Who makes the decision as to which CIWS to purchase? The MOD? Could I, as a logistics officer, be involved with this decision?
So, the "user", in this instance Navy Command would generate the 'requirement'. For Navy specific equipment the MAR CAP DEV area would progress this, for a joint enabler a capability 'CAP' branch in JFC would, taking a requirement from Joint User.
With a requirement the CAP areas would prioritise it and then run an option to seek new money from the Equipment Programme, once that is succesfully secured (hard to do), the requirement plus the money (promise of) are sent to a delivery team in DE&S (Abbeywood) or JFC ISS. It's the delivery team who make the decision over what "kit" meets the requirement. You can see there are two clearly deliniated roles: one creating the demand, the requirement and another satisfying that requirement with a solution.
So, you asked who does this and could a Loggie get involved,the simple answer is yes but typically only for Loggie equipments or applications wherein there is a joint CAP team for logistics applications and equipments and in DE&S there are logistics focussed delivery teams with embedded Logistics Officers.
Capability Development and Acquisition are streams of a second stage career you can delve into more deeply, if you had that urge and you can get in-service MSc education too.
An appointment/draft to Abbey Wood is a very useful stepping stone to a second career. As a PWO I found it invaluable in preparing for life post the RN. I also decided to study for an MBA while at Abbey Wood and have gone on to find full and challenging employment after my life in a Blue Suit. There are thousands of buzzes about how servicemen/women at DE&S have secured future employment by favouring a particular supplier, but in my personal experience the best way of securing employment is by displaying integrity coupled with specialist knowledge. Good luck with your future career, but as with everything else in life - timing is critical.
I'll qualify 'pastrdp''s comments, the right post/draft in DE&S or ISS will help with future employment, but suppliers/industry can then look at you - it works both ways; plenty of people have decided to jump and approached companies only to find they've not liked what they've seen, but in general DE&S is good exposure to commercial practise and sectors of industry that may interest.
It also shows you quite often that industry is no better than the RN....
I hope you don't mind a pongo jumping in with an opinion!
Being involved in bringing on the next generation of equipment is vitally important and something all Services should be involved in to ensure the right kit is in the right place at the right time.
However, I feel it is more important for the OP to become a naval officer with a thoroughly professional in-depth knowledge of how the RN operates so that he/she can then feed into any design process. Development companies can hire any number of bright people; the Service needs people with that thorough knowledge of the end-user environment to ensure the wonderful new bit of magic actually works in the way needed.