I've got a few patches of fibre print through on a piece I've just finished. i am not too worried about the visual finish and am clear coating it anyway, but I just wanted to check if this was going to compromise the part in any way, i.e. structurally or longevity, or if it is purely an aesthetic issue?

Would it be worth brushing over some resin in the print through areas and flatting back, or am I OK just to go ahead with the clearcoat?

Print-through itself is purely an aesthetic issue, however it can also be a symptom of something that could indicate compromised strength - for example a part that has been exposed to heat well above it's operating temperature will likely print quite badly, and that heat may have compromised the strength of the component. 

In most cases though, purely cosmetic issue and don't need to worry about it. As for whether you can bury it in clear coat, again in most cases I would say yes - in severe cases I would say you may need to add some resin to build enough thickness to fill the low spots properly. Clear coats will also shrink back quite a lot compared to resins, so you may find that immediately after spraying the part looks flawless and then 3 or 4 days later you start to see the print reappearing. With a good layer of clear you can normally just wet-sand and polish that out.