The manual you are reading must be a pre V4.0 one as the Mitel 5000 is just called a 5000 now, also you don't get 5 licenses (in the UK anyway) you get either 16 CAT D licenses which will allow you to equip the system with up to 16 Mitel 53xx phones. Or a DDM16 which will allow you up to 16 digital phones. As starter packs.
If you are working on an existing system get into DB programming then click on Help / About Software License
You will then see a list of what licenses the system has:
A, Old style Inter-Tel IP Phones
B, Old Style Softphones
C, Can't remember
D, Current Style Mitel IP Phones
E, Digital Phones Post V4
F, SIP Phones, SIP Softphones
So yes as Marcolive already posted you need a license for ever live phone.