Hi Jon,
I would expect it to vary by field and by type of institution (industry vs academia). I would expect the industry trials that are missing to be the ones with unfavourable results. I would expect the missing trials by independent academics perhaps to be those with dull results or to be small trials that failed to recruit. I may be wrong.
I think in fields where most studies are done by pharmaceutical companies, it would be reasonable to assume that systematic reviews that don't include all trials (e.g. those that don't actively look for unpublished trials) will overestimate benefit.
Best wishes,
Tom