If they blocked Signal just because it was less of a trouble to block compared to WhatsApp, then all the people that were on Signal will easily switch to WhatsApp... What you have at this point, is a government paying the price of blocking a less popular messaging app they cannot control, while the people they are after can just switch to a MASSIVELY used messaging app the gov can also not control and additionally, is too expensive to block.
If this was the case,it would actually work against the gov. Do not underestimate gov authorities, they are not THAT naive. If they had not blocked Signal at all, they could at least track Signal users and at least have that information: that this small group of people (Signal users), contains the group of people they are after. They could have their honey pot there. Mixing the "dangerous" Signal userbase with the chaotic massive userbase of WhatsApp makes no sense, unless you really have WhatsApp on your side.
I hope you understand what I am trying to say.
edit: rephrasing