It says here that before their forced conversions Portuguese Jews had "easily recognizable" names (I don't know if that's true) and it gives a long list. It also says:
Como característica geral, os nomes judeus nunca têm patronímicos à
portuguesa, se bem que pelo menos os nomes antecedidos por ben o
pareçam ser. Como é o caso, por exemplo, de Benafaçom, que
significaria filho de Afaçom. Na verdade, só encontrei três judeus com
nomes de família que podem ser patronímicos à portuguesa: Marcos,
Vicente e Manuel, se bem que este último nome também apareça como
Manueell. Claramente patronímico português só encontrei um, aliás
associado a um primeiro nome cristão. Trata-se de Álvaro Gonçalves,
judeu, morador na cidade de Évora, que a 15.10.1454 teve perdão da
justiça régia pela fuga da prisão. Mas julgo tratar-se já de um
converso (ou um dos vários que, como vimos, foram por certas pessoas
obrigados a converter-se), ou então um descendente de judeus de
Castela, onde as conversões forçadas começaram em 1391 e desde 1449
estavam em vigor os estatutos de pureza de sangue.
The idea that Jews in the Iberian Peninsula all changed their surnames to names of trees or of geographical accidents is widely considered to be a myth. Converts had to be baptized, so many adopted the surnames of their godfathers; others just chose common surnames (they were trying to blend in, not stand out!).
According to Wikipedia the Spanish patronymic suffix -ez (-es in Portuguese) seems to have ceased being productive in the 13th century. There are no sources there, but I've read the same elsewhere, simply stating that from 1200 onwards the surnames in -ez had become more or less fixed. This is well before the Inquisition and the forced conversion of Jews.
This still doesn't explain why there seem to be no patronymics in -es formed from Hebrew names. Browsing several lists of medieval Iberian names reveals a possible reason: there seem to be no or very few personal names of ultimately Hebrew origin ending in -el at the time. There are people called João, José, Mateus or, in Spanish, Juan, José, Mateo (that is, the old forms of those names), but among the lists one has to go until later to find some instances of people named Miguel and Gabriel. Could it be that these only became fashionable after the end of the Middle Ages? Finding this out would require sources that I don't have.