I remember reading that OS v3 will allow you to return to the application you where using when you automatically switch to something else like a phone call.
This means that something stays in memory, which could - supposedly - slow down something.
However, the amount of installed applications (unlimited in OS v3 I understand) will only slow down spotlight..
Apps are not like processes running on a PC, they are stored in flash memory like a HD on a PC. So Apps would be no different than music stored in flash memory,.. so no it shouldn't slow down.