The way the projects are applied in the game's resource files 1 suggests that the level of the agent does not have any effect on the bonus – it's strictly the number of unassigned agents.
In the case of the Reconnaissance/Support projects, a risk is calculated based on the participating agent's level and the defense modifiers of the target city (i.e. counteragents). Then, when one of these projects is active, the risk of failure/negative detection outcome is reduced by the operation's perk modifier multiplied by the number of agents at the HQ.
The default multiplier for both the mentioned project types is 1 2, so having 5 agents at the HQ would reduce the risk of failure (increasing your chance of success) by 5%. Note that the outcome is restricted to a range of [10, 90]
, so even with a lot of agents you could still fail a Very Easy mission, for example.
The other projects work similarly, although in those cases the percentage modifier is more clearly stated.
1. See assets/Gameplay/Lua/ConvertOperationsSystem.Lua:L309
2. See assets/Gameplay/XML/Civilizations/CivBEPlayerPerks.xml:L1625