"I wish you had a pleasant stay here"
means I know you are not having a pleasant stay here right now, but I wish it were not so.
"I wish for you to have a pleasant stay here"
would be the full version or, in the present subjunctive, "I wish you have a pleasant stay here", which is archaic in style. You could rewrite it to say, "It is my wish that you have a pleasant stay", which uses the present subjunctive and is not archaic.
"I hope you have a pleasant stay here"
should take the present subjunctive as well, but it's not used in Modern English like that. Nowadays, "hope" almost always takes the present indicative:
"I hope he has a pleasant stay."
"I hope that he have a pleasant stay."
"I pray that he have a pleasant stay here."
"Wherefore, the defendant prays this court be moved to grant this
(Opening of Modern English "wherefore" clause in legal briefs and motions)
Shakespeare often used a present subjunctive verb when using the verb "hope", but that is almost never the case today. This is the reason why your grammar book is having a problem showing you this example and comparing it to "wish" but with no "verb". It's because "wish" still takes a subjunctive in Modern English (although never in the present subjunctive when "wish" is a verb), whereas "hope" does not take a subjunctive in "Modern English".