The simple answer is no, Deadpools rights were not included with the X-Men in the deal that effectively granted Fox perpetual rights to make movies based on the X-Men and ancillary characters. Deadpools rights were sold in 2000 to Artisan Entertainment as part of a larger agreement that encompassed more than a dozen Marvel characters. In the pre-Marvel Studios days, Marvel would strike a deal with pretty much anyone who thought they could produce a film based on one if its characters. For instance, Black Widow almost had her own solo movie before any of her fellow Avengers.
Artisan was purchased in 2003 by Lionsgate, and the Deadpool project appeared to be going nowhere. The following year, however, New Line Cinema, which produced the Blade movies, took an interest in the character. David S. Goyer, who wrote the Blade films, including the then just-released Blade: Trinity (co-starring Ryan Reynolds), spoke in 2004 about tackling a Deadpool movie:
I want to do something else with Ryan Reynolds because I really loved working with him and New Line wants to do something else with Ryan Reynolds and Marvel wants to do something with Ryan because there arent a lot of actors anymore that can do credible action and be funny and that are also good actors
The New Line version of Deadpool would specifically not be connected to the Fox films, as Goyer noted:
We would completely reinvent it. We cant connect it to Weapon X or anything like that. Well see.
New Lines interest went nowhere, and in 2005, Fox became involved, and eventually signed a deal for Deadpools movie rights. The character was included in 2009s X-Men Origins: Wolverine, where he was portrayed by Reynolds.