I've been pondering this question myself a lot recently, especially in the context of hospital epidemiology. My thoughts below:
The Case for Counts:
The real core of the strength for counts is that they're a more meaningful number on a practical scale. Tell a nurse they're going to see 0.20 cases/patient-day more infections and they'll give you an odd look. Tell them they're going to see 17 more cases this month? That's a meaningful number for them to work off of.
This ties into a general undercurrent in Epidemiology at the moment focusing on an interest in absolute numbers, because our currently reliance on relative effect measures does some funny things, including exaggerating small effects at times. For example, if your rate doubles is that a crisis? Probably depends on if the counts are 1 and 2, 100 and 200 or 100,000 and 200,000.
The Case for Rates: That being said, there's a reason people like rates. Counts only really make sense if your denominator is fixed, or relatively so. For example, if your clinic sees 1,000 patients each month, then a change in cases from Month X to Month X+1 is a genuine change in cases. But if you saw 1,200 the second month? Are your increase in cases an increase, or just having more opportunity to see cases? Or in the case of hospital acquired infections, if you had more patients staying for more time in a given month, you had more opportunities to get them sick, and should probably adjust for that.
So the answer I think, sadly, is it depends. If you're confident that your denominator is stable, and each time point represents the same "opportunity" to see cases, you can probably get away with cases. But if it moves around, and one time point has more patients, staying for more time, etc. then you should probably use rates, unless you don't think you can get a good denominator.
And on a practical note, clinicians are trained, in my experience, to expect rates. If you want to publish or distribute your count-based findings, expect some push-back.