I assume the Typhon Pact novels will at least touch on the topic of cloaking devices and their status in the post-Destiny landscape of the UFP. We know that the Federation has cloaking tech. According to JM Dillard's Resistance, each ship's computer is equiped with the spec's to make one with available components, and with permission from an Admiral. Since we don't know the exact wording of the Treaty of Algeron, it's impossible to say whether the treaty is now null and void. With the IRS being an official ally now, it gets even trickier.
Even if it is deemed that Federation ships can have cloaks, I would still prefer they don't use them very often. Talk about a deus ex machina
. The Federation is about exploring out in the open. Not hiding in the shadows. The group within the Federation/Starfleet that could really benefit from cloaking tech is Section 31, but as they are already super secretive and "underground", it's safe to assume they already use some form of cloak. According to DS9, they have their own ships, and they need some way of hiding them during their operations. As a clandestine group who do whatever is neccesary to secure the Federation, it would be ludacris for them to not use cloaking tech.