I've found studies that cover ZIP and staged analysis such as: Yogita S. Wagh & Kirtee K. Kamalja (2018) Zero-inflated models and estimation in zero-inflated Poisson distribution, Communications in Statistics - Simulation and Computation, 47:8, 2248-2265, DOI: 10.1080/03610918.2017.1341526
What I can't seem to find is anyone comparing juvenile abundance and year class data to adult abundance using similar but different size gears in different environments and/or at different scales. I've found something close here: Ali Arab, Mark L. Wildhaber, Christopher K. Wikle & Casey N. Gentry (2008) Zero-Inflated Modeling of Fish Catch per Unit Area Resulting from Multiple Gears: Application to Channel Catfish and Shovelnose Sturgeon in the Missouri River, North American Journal of Fisheries Management, 28:4, 1044-1058, DOI: 10.1577/M06-250.1
I've found out that part of the answer is already in answers to this question.
What are some of the most important, or most cited, papers within hurricane research?
In anticipation of one criticism of the question: Should we allow requests for references?