The next generation of GNSS promises new satellite constellation and signal designs that will improve capabilities and performances for all users. Frequency Hopping Modulation (FHM) is one of the signal designs that is being considered due to its potential robustness against interference and multipath. In this work, we assess the impact of the ionosphere on coherent FHM signals. In particular, we look at the waveform and autocorrelation properties of the FHM signal before and after passing through the refractive ionosphere channel. Then we highlight the ambiguity between code phase and ionosphere total electron content (TEC) effects on the received signal, and we discuss acquisition performance of such signal parameters for two coherent FHM signal designs: 1) using a 2-ary hopping sequence between 1227.6 and 1575.42 MHz, and 2) using a 19-ary hopping sequence of evenly-spaced frequencies between 1227.6 and 1267.6 MHz.