The PreFixes have definitely helped me enormously.
Here are some a few things that may not be so obvious before you start using them and while Colours would be great....still would not help with these.
Firstly, the BO Attribute List.... Notice how all the References and Shortcuts are grouped together. Makes it much easier to not only FIND what you are looking for but also... understand what type of Reference it is just at a glance.

Secondly....
Imagine the following BO structure.....

Without using PreFixes your BO Attribute lists would looking something like this....
TENANT
TenantName
DateCreated
Status
Countries
COUNTY
Country
OfficeAddress
Tenant
Entities
ENTITY
EntityCode
EntityDescription
Country
Departments
DEPARTMENT
DepartmentCode
DepartmentDescription
Entity
Resources
RESOURCES
ResourceCode
ResourceName
Department
In such a simplistic model it is not hard to recognise what is what but that ONLY comes from an understanding of the Business Object structure and the Attribute names. Now imagine that instead of a few trivial Attributes.... you have 50 or 100 Attributes.... Good Luck remembering which are References at all let alone what type of Reference it is.
Additionally.... Imagine being deep in a Process and you need to FIND Resources for a particular Tenant... try building that Action and selecting from 100s of Attributes.

Essentially when navigating in this scenario, you are always looking for the Parent Business Object. Hence, if we had used PreFixes... then it is significantly easier...
The BOs look like this....
TENANT
TenantName
DateCreated
Status
om_Countries
COUNTY
Country
OfficeAddress
ob_Tenant
om_Entities
ENTITY
EntityCode
EntityDescription
ob_Country
om_Departments
DEPARTMENT
DepartmentCode
DepartmentDescription
ob_Entity
om_Resources
RESOURCES
ResourceCode
ResourceName
ob_Department
And navigating while buried in a Process requires not thinking AT ALL.... All you need to do is type ob in the inspector and the Parent BO is presented as the right choice for EVERY Level...
FIND Resource WHERE Resource.obDepartment.obEntity.obCountry.obTenant=ThisTenant