My girlfriend has been separated for 16 years - if she dies is her husband entitled to her estate
Yes, he would be, assuming that she does not have a will.
If she dies intestate (without a will) her spouse would inherit the estate. If she is worried about that, she should either get a divorce, or have a will prepared that leaves her estate to others.
Sad but true. Please advise if I can of assistance in preparing a Will.