Persistence and extinction are key processes in infectious disease dynamics that, owing to incomplete reporting, are seldom directly observable. For fully immunizing diseases, reporting probabilities can be readily estimated from demographic records and case reports. Yet reporting probabilities are not sufficient to unambiguously reconstruct disease incidence from case reports. Here, we focus on disease presence (i.e. marginal probability of non-zero incidence), which provides an upper bound on the marginal probability of disease extinction. We examine measles and pertussis in pre-vaccine era United States (US) cities, and describe a conserved scaling relationship between population size, reporting probability and observed presence (i.e. non-zero case reports). We use this relationship to estimate disease presence given perfect reporting, and define cryptic presence as the difference between estimated and observed presence. We estimate that, in early twentieth century US cities, pertussis presence was higher than measles presence across a range of population sizes, and that cryptic presence was common in small cities with imperfect reporting. While the methods employed here are specific to fully immunizing diseases, our results suggest that cryptic incidence deserves careful attention, particularly in diseases with low case counts, poor reporting and longer infectious periods.