I think it would depend on the particular context, but at least in Hubert et al 2000 the meaning is fairly clear:
This was a 2-year study, with 14-, 29-, and 53-week interim necropsies and a 106-week terminal necropsy. Before study initiation, 20 rats/sex/group were selected to be euthanized at each interim necropsy; all remaining surviving rats were euthanized at terminal necropsy.
Terminal necropsy in their case is referring to the last batch of necropsies in the study: terminal referring to the study duration, rather than the time relative to the life of an individual.
Usage is the same in Monath et al 2010.
In other cases, like Toyama & Yuasa 2004, the term seems redundant with no useful meaning besides "necropsy," though it would be fair to note that the necropsy is still occurring at the end of the study, they just don't have multiple time points.
Hubert, M. F., Laroque, P., Gillet, J. P., & Keenan, K. P. (2000). The effects of diet, ad libitum feeding, and moderate and severe dietary restriction on body weight, survival, clinical pathology parameters, and cause of death in control Sprague-Dawley rats. Toxicological Sciences, 58(1), 195-207.
Monath, T. P., Lee, C. K., Julander, J. G., Brown, A., Beasley, D. W., Watts, D. M., ... & Levesque, P. (2010). Inactivated yellow fever 17D vaccine: development and nonclinical safety, immunogenicity and protective activity. Vaccine, 28(22), 3827-3840.
Toyama, Y., & Yuasa, S. (2004). Effects of neonatal administration of 17β-estradiol, β-estradiol 3-benzoate, or bisphenol A on mouse and rat spermatogenesis. Reproductive toxicology, 19(2), 181-188.