Uruguay defender Lugano was left out of the squad that lost 1-0 to Southampton on Saturday after making a long-haul international trip to Japan during the week.
Vydra, who scored 20 goals for Watford last season, was also away on international duty with the Czech Republic and only managed seven minutes as a substitute against Saints.
Clarke told the club's official website: "I didn't include Diego in the squad at all on Saturday after he travelled with Uruguay and went to Japan.
"When he came in to the club, he was a little bit behind us in his preparation.
"Vydra - I have to be honest - I haven't seen much of. He came in for his medical last week and then went away with the Czech Republic.
"I thought he looked quite lively when he came on and I know he's done a full pre-season with Udinese, so I think Matej will pick up the pace quickly."