Oh dear God - in addition to what we're all worrying about - here I am on the laptop- in shock and feeling quite sad.
Other than feeling really shocked and saddened I'm truly at a loss
You've known this man for a little more than a year, you've not met his estranged STEPSON (he's not even actual son) and he has had little more than sporadic with him in 30 years either.
Quite honestly, I find your emtional reaction to this is odd, and excessive and misplaced. 
I must also say my partner mentions them from time to time - always in a fond manner and always respectfully
I find this unusual. My DH and I both have ex-spouses from 30 years ago (no children from those marriages) and we almost never have a reason to mention our exes to one another, and haven't done in probably 28 of the 30 years since we both got divorced and got together. While I am sure he occasionally googles/FB checks her to see what she's up to, as do I with my ex, purely out of curiosity, we certainly don't feel the need to discuss it with one another.
I had thought of quietly contacting the stepson as maybe he felt split into choosing loyalty to his mum - which is understandable but life is short and it saddens me that some families function this way
That would be weird and interfering. They are NOT a family. He was with this woman for a relatively short time by the sounds of things. Once the relationship ended there was obviously no pretence or effort to keep this father/son thing going, whether that was his choice or not. It is not the same as feeling an obligation to, or deep longing for a relationship with a biological child, unless he literally brought this boy up from a baby for many years, much like an adoptive parent would. Even if he did, the lack of contact for thirty years would mean this man would barely remember him being his 'father' and living at home anyway. I doubt very much he considers him his father at all.
I have an estranged step sibling and half sibling from my father's second marriage who I have had very little contact with since childhood, because contact with my (now deceased) father was always very sporadic. I know where they are and they know where I am - we could find each other if we wanted to, but apart from seeing one another when he died, we have just never felt the need to make a big deal about being 'family.'
I've nothing against them, I wish them well, we just aren't close - more like distant cousins. I would think it was pretty fucking weird if some random person who'd been involved with my step/half sibling for only a year started messaging me to try to involve me in their lives now, after 40 years.
I did not feel it fair to do this to my partner without discussion - also the relationship is quite new.
You are right about that. Don't overstep boundaries.
I now wonder what would the repercussion be if I don't say and he somehow finds out- I feel I'm damned if I do or if I don't?
There won't be any repercussions. Why on earth would there be repercussions? He hasn't seen her for THIRTY YEARS. He left her. He didn't love her any more. This is madness.
One side of me feels it would be intrusive, it's not my business and it would cause pain
Yes it would be intrusive and no it's not your business. It wouldn't cause pain so much as bewilderment I imagine.
It's just really sad the mum (his ex) has passed away and he (my partner) is oblivious to that fact.
Again, absolutely nothing for you to be feeling so sad about. Do you react this way over everything? Because it's not normal.