#1 means "you should be in bed now". #2 is incorrect. #3 is close to "you should have been in bed then", but in opinion it is incorrect, mixing past tense with supposition in the present tense.

I believe all three are wrong. I do not believe in this case that past subjunctive mood ("were") is appropriate. There is no conditionality. Since there is no imagined situation the present tense should be used. Subjunctive mood in present tense can be defended since there is an expressed wish. I would say "It is time for you to be in bed." or "It is time that you be in bed." (subjunctive) or "At this time you should be in bed".

The three sentences differ in their tense and meaning: "It is time you were in bed" is in the subjunctive mood and suggests that the action of going to bed should have already taken place. It implies that it is late or past the usual bedtime, and the speaker is reminding the listener to go to bed now. The use of "were" in the subjunctive mood indicates that the speaker is making a suggestion or recommendation, rather than stating a fact. "It is time you are in bed" is not grammatically correct, as it mixes the present tense "are" with the phrase "it is time," which implies that the action should have already happened. The correct form would be "It is time for you to be in bed," which indicates that the listener should be in bed now or soon. "It was time you were in bed" is in the past tense and suggests that the action of going to bed should have taken place earlier. It implies that the speaker is reminding the listener of a missed opportunity or an action that should have been taken earlier. The use of "were" in the subjunctive mood indicates that the speaker is making a suggestion or recommendation in the past.