My understanding - and correct me someone if I'm wrong - is exactly what you said - only those items with a scan time of 0 will be scanned every time a user logs on.
Yes the machine will enter the queue, but probably only for a few seconds if there is nothing to scan.
The only issue I see is if your queue gets so large that by the time Lansweeper is ready to scan the machine it has been swicthed off in which case you may get errors as it cannot communicate with the PC.
Or if you have the premimum version you could use active scanning or scheduled scanning and do away with the logon script...?
Finally, as an alternative you could add some inteliigence to your login script that woudl only trigger a scan if certain criteria were met - ie if a logon had already taken place that day set a variable somewhere or write a file somewhere etc.
Just my thoughts any way!