The pirates with cloaks in WC4 were given them by Tolwyn, as part of his stirring up trouble to create cause for a war. It's not, fanfiction aside, something to which a pirate would have ready access, without outside help.
As for cloaking, of the 7 cloak-equiped recon Excaliburs sent into the Kilrah system to investigate contact being lost with in-system bases, only the 7th, flown by Maj. Washington, survived, possibly because the bugs had moved on by that point, as all he saw was battle debris. (ICIS manual).
The Dragon's lack of availability post-WC4
has been discussed before, but the short form is that a) given its use as a terror weapon (biowarfare and incinerating civilian ships from the inside out are hardly SOP for Confed), the political costs outweighed the benefits, and b) the Dragon was prohibitively expensive for mass production, thanks to all of the advanced technologies included in it (cloak, capship-style matter/antimatter powerplant, and so forth).
Besides, in just about every way, the Dragon's performance was met or beat by the ships we did get in WCP, let alone WCSO (where even the WC3 retreads like the Excalibur and Thunderbolt got upgraded). Not paying Dragon prices for Dragon performance is definitely an issue in a Confed with a budget where the military has to fight for every dime (per ICIS manual).