I often comer across the term high fidelity in QM papers. Does fidelity imply ratio of entangled photons / total photons? Is there some other metric to measure how good the source is?
Fidelity is a way of quantifying how similar 2 states are to each other. Fidelity $F$ is by definition $F\in[0,1]$, with $F=1$ meaning that 2 states are identical and $F=0$ means they are as different as physically distinct possible.
Fidelity is often used as a way of saying how good your source or quantum state preperation is, by comparing the state of what you measure with what you ideally want.
As an example, if you wanted to create pairs of perfectly entangled particles (as you alluded to) and you had extra stray (non-entangled) photons that you measure in your ensemble/group of prepared bi-photons, then your mixed or ensemble averaged state will be different then what you want (perfectly entangeld bi-photon pairs) and how close you are is given by $F$.