I used clamwin 0.88.9 and organized updating from the local web server (Apache) by creating virtual host database.clamav.net, which contained main.cvd and daily.cvd. All was OK: clamwin 0.88.9 was updated every day by downloading daily.cvd from the virtual host.

But after update to virsion 0.90 clamwin database files began to include the folder daily.inc without daily.cvd.
How I can create working updates clamwin 0.90 from the local webserver (what the necessary folders I must create)?

you can still use main.cvd and dialy.cvd, clamwin will attempt to use diffs but when not found will revert back to the cvd files. You will get some warnings and errors from database update process but it will update (the error messagesd will be removed in the next release coming soon).