In eshell:

~ $ history

    1  history

~ $ eshell/clear

[...]

~ $

[...]

~ $ history

    1  history

    2  eshell/clear

    3 

[...]

    4  history

An easy (dirty?) way to fix it could be override eshell-input-filter (from em-hist.el):

(defcustom eshell-input-filter

  (function

   (lambda (str)

     (not (string-match "\\`\\s-*\\'" str))))

  "Predicate for filtering additions to input history.

Takes one argument, the input.  If non-nil, the input may be saved on

the input history list.  Default is to save anything that isn't all

whitespace."

  :type 'function

  :group 'eshell-hist)

to:

(defcustom eshell-input-filter

  (function

   (lambda (str)

     (not (string-match "\\`\\s-*\\'" (string-trim-left str)))))

  "Predicate for filtering additions to input history.

Takes one argument, the input.  If non-nil, the input may be saved on

the input history list.  Default is to save anything that isn't all

whitespace."

  :type 'function

  :group 'eshell-hist)