Simple bash script creates apache2 virtualhost config for subdomain
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 &gt;/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=$( wc -w &lt;&lt;&lt;"$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." &gt;&amp;2
    exit 1
fi

read -p"Create virtualhost (= Folder name,case sensitive)" -r host
case "$host" in
    "")            echo "Bad input: empty" &gt;&amp;2;      exit 1 ;;
    *"*"*)         echo "Bad input: wildcard" &gt;&amp;2;   exit 1 ;;
    *[[:space:]]*) echo "Bad input: whitespace" &gt;&amp;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 &gt;"$tmphost" &lt;&lt;EOF
&lt;VirtualHost *:80&gt;
    ServerAdmin webmaster@localhost
    DocumentRoot $dir
    ServerName  $host.localhost
    ServerAlias $host.localhost
    &lt;Directory "$dir"&gt;
        AllowOverride All
        Require local
    &lt;/Directory&gt;
    # Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
    # error, crit, alert, emerg.
    LogLevel warn
&lt;/VirtualHost&gt;
# 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 &lt;&lt;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




Responding to your questions:


"determine if running in a terminal?" Yes with this obscure test:

if [ -t 0 ]; then echo "in a terminal"; fi


That tests file descriptor 0, which is stdin. If you're launching your script as a GUI, that test should be false.
editor=${VISUAL:-$EDITOR} sets the editor variable to the user's $VISUAL variable, or if that's not set, to the $EDITOR variable. Many programs use this to determine the user's preferred "terminal" editor. vim and emacs are two common values there. If neither of those are set, then the user gets to go edit that however he chooses.
"is read terminal only?" Yes


If you're going to aim for GUI and text versions, I'd use one script, but make sure all the common code is put into functions so you don't have to duplicate your code. For example:

get_virtual_host() {
    if [ -t 0 ]; then
        read -p "Create virtualhost (= Folder name,case sensitive)" -r host
    else
        host=$(zenity --forms --add-entry=Name --text='Create virtualhost (= Folder name,case sensitive)')
    fi
    case "$host" in
        "")            echo "Bad input: empty" &gt;&amp;2;      exit 1 ;;
        *"*"*)         echo "Bad input: wildcard" &gt;&amp;2;   exit 1 ;;
        *[[:space:]]*) echo "Bad input: whitespace" &gt;&amp;2; exit 1 ;;
    esac
    echo "$host"
}

host=$(get_virtual_host)