There are ways to make this faster, but would require a lot of configuration if you have 1000 subnets.
Under Configuration go to Scanning Methods (which I'm sure you've already been here). For each of the IP scan ranges use the following tips. But take note of any performance issues that may come from the following changes as they may not work the best, or be practical, in all environments.
Tip 1: The more narrow the range the faster it will scan since it does not have to scan IP's that have nothing on them.
Tip 2: Change the timeout to 1 instead of 4, this will fail unused IP's faster.
Tip 3: Check No Windows for any subnet you know does not have a windows device (printers, wyse terminals, etc). This will skip trying to do any WMI queries which in turns doesn't have to wait for a fail response.
Tip 4: Use the schedule column. You can't tell it to stop at a certain time, but you should be able to set them up well enough that all ranges are done by the time the work day starts.
Tip 5: Under 'Server Options' increase the number of simultaneous IP address scans. Default is 12, 20 should be fine (depending your scanning server). I believe you can increase it higher, but you may not want to.
I do not believe there is a way to stop active scanning during the day (well, supported at least), but you can increase the Minimum Time Between Scans to more than 20 hours so that devices aren't scanned every day. Also increasing the Check Interval from 15 minutes to 30/60 minute or even 4 hours may also help.
An unsupported way to do it would create a scheduled task to start and stop the Lansweeper service so that it is not running during the day. This would force Lansweeper to start a full active scan every time the service started though and may cause more harm than good.
-Kris