The payment on NI contributions by your employer is completely a non issue and should not be brought into any discussions that are had - that's completely non of your business being frank.
my boss hasn't paid any NI Contributions since I started working for him, BUT he has been deducting the money from my pay each month.
What is an issue is if he has not been submitting your payslip totals to hmrc (to document your contributions and what he owes) this could very possibly be the case and is the issue that needs to be resolved.
Personally my recommendation would be to broach the subject directly with hmrc if your boss is being at all evasive, it's an issue between them and him and i would be 99% certain this will be resolved in your favour - the only fly in the ointment would be if your boss suddenly vanished you may have to provide reasonable evidence to hmrc.
Note there would be no presumption in my mind that you boss has done anything wrong simply due to the figures not appearing on hmrc's computers - hmrc aren't exactly a reliable source of anything - albeit they like to pretend their systems are pretty good - they are not and the lack of anything means nothing until a full investigation has been done. I would complain directly to them that the info isn't showing up and that you want that investigated asap - the ball is 100% in their court as to how the proceed in that regard.
If you boss isn't shifty they should be able to confirm details of RTI submissions made - its a fact they have been submitted or not - if you are asking him ask him to provide confirmation of RTI submissions - although personally i would solve via the hmrc route.
My question is, where do I stand on this from a liability point? All my payslips show that my NI and tax has been getting deducted every month, but am will HMRC still see me as being liable for the tax if it hasn't been paid, despite the fact all my payslips show that it has been??
I wouldn't worry - the fact that you will be highlighting the issue to hmrc (if it needs to be) and as long as you have reasonable proof everything will be sorted - historical payslips and matching payments via bank each pay period is about as good a proof as you can hope for.
Hopefully this is just hmrc being it's normal hopeless self - it is very poor form if hmrc have presumed that if the figures don't show up on their system from an initial phonecall or online check then the figures aren't in their possession. My presumption would be they have the info unless the employer can't substantiate this fact. Note i am not saying he has submitted everything to hmrc - it may be the case he hasnt - but its better to start with the presumption this may be a simple processing error rather than something more serious.