Notes:

• Quote your variables. Ref Security implications of forgetting to quote a variable in bash/POSIX shells

• Don't use ALLCAPS varnames. It's too easy to overwrite important shell variables like PATH.

• A2ENSITE=$A2A2ENSITE$HOST".conf" -- I don't see the A2A2ENSITE variable anywhere

  • this is a perhaps a corollary of the ALLCAPS vars problem: they can be hard to read.

• For Command Substitution, don't use backticks, use $( ... ). That syntax is (IMO) easier to read, and there are other advantages, such as nestability.

• if ((`which zenity|wc -w` == 0)) -- use the bash builtin type command to see if there is a zenity command available: type -p zenity will return an unsuccessful exit status if there's no zenity in your path:

    if ! type -p zenity >/dev/null
  

  Although I don't really see the need for zenity. It would be super frustrating for the user who doesn't have it, being prevented from using your script. And the technical user who would be comfortable installing it is the type of user who doesn't need the bells and whistles, IMO.

• To check if a string is empty, you don't need to call out to wc.

  Not this:

    TEXT=`zenity --text-info --filename=$TMPHOST$HOST --editable`
    words=$( wc -w <<<"$TEXT" )
    if (($words == 0))
  

  but this:

    text=$(zenity --text-info --filename="$filename" --editable)
    if [ -z "$text" ]       # cancel if empty
  

• use mktemp for temp files

    tmphost=$(mktemp)
  

  And just use "$tmphost" instead of $TMPHOST$HOST

• you can tell bash to automatically delete the temp file when it exits:

    trap "rm $tmphost" EXIT
  

• validate user input for host: a case statement might make sense here:

    host=$(zenity --forms --add-entry=Name --text='Create virtualhost (= Folder name,case sensitive)')
    case "$host" in
        "")            zenity --error --text="Bad input: empty";      exit 1 ;;
        *"*"*)         zenity --error --text="Bad input: wildcard";   exit 1 ;;
        *[[:space:]]*) zenity --error --text="Bad input: whitespace"; exit 1 ;;
    esac
  

• I applaud your use of here-documents

• use if [ "$(id -un)" = "root" ] instead of the USER variable.

• mkdir -p silently does nothing if the directory already exists, so you don't need to test -d

Perhaps you want this:

#!/bin/bash

webroot="/home/leonid/Web/" # root folder where subfolders for virtualhosts created
apachehost="/etc/apache2/sites-available/050-" # prefix for virtualhost config file
a2ensite="050-"             # short prefix for virtualhost config file
tmphost=$(mktemp)
trap "rm $tmphost" EXIT

if [ "$USER" == "root" ]
then
    echo "You should not run this script as root but as user going to edit web files." >&2
    exit 1
fi

read -p"Create virtualhost (= Folder name,case sensitive)" -r host
case "$host" in
    "")            echo "Bad input: empty" >&2;      exit 1 ;;
    *"*"*)         echo "Bad input: wildcard" >&2;   exit 1 ;;
    *[[:space:]]*) echo "Bad input: whitespace" >&2; exit 1 ;;
esac

# braces only for readability
hostfile="${apachehost}${host}.conf"    # apache virtualhost config file
dir="${webroot}${host}"                 # folder used as document root for virtualhost

# virtualhost template 
cat >"$tmphost" <<EOF
<VirtualHost *:80>
    ServerAdmin webmaster@localhost
    DocumentRoot $dir
    ServerName  $host.localhost
    ServerAlias $host.localhost
    <Directory "$dir">
        AllowOverride All
        Require local
    </Directory>
    # Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
    # error, crit, alert, emerg.
    LogLevel warn
</VirtualHost>
# vim: syntax=apache ts=4 sw=4 sts=4 sr noet
EOF

# edit virtualhost config
editor=${VISUAL:-$EDITOR}
if [ -z "$editor" ]
then
    echo "edit '$tmphost' to your liking, then hit Enter"
    read -p "I'll wait ... "
else
    "$editor" "$tmphost"
fi
# probably want some validating here that the user has not broken the config

echo "execute root tools with pkexec to create virtualhost"
mkdir -p "$dir"

pkexec /bin/bash <<EOF
chgrp www-data "$dir"
chmod u=rwX,g=rX,o= "$dir"
mv "$tmphost" "$hostfile"
chown root:root "$hostfile"
chmod u=rw,g=r,o=r "$hostfile"
a2ensite "${a2ensite}${host}.conf"
EOF