b) Checkbox in "copy dialog" "dont refresh folder after an action will be done" - this way you can copy one file to another 10000 on server and immediately go to parent dir
You can achieve same, if you stay in parent directory and add the subdirectory name to "target directory" box on upload dialog.
btw, There is a bug in winscp 3.4.2 build 197 russian windows 2000 server - when you try to copy MULTIPLY (not one) files to folder, which contains ~>10000 files, winscp tells you "No argument for format %s" and no dialog appears. Maybe thereis some troubles in translation file ("%s"...?)
It was really a bug in translation file. I hope that it is already fixed, please try to download the latest translation file.