"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."
(Modern English)
"I hope that he have a pleasant stay."
(Shakespearean English)
HOWEVER:
"I pray that he have a pleasant stay here."
(Modern English)
"Wherefore, the defendant prays this court be moved to grant this
motion."
(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".