For all trains (and especially night trains) it is advised to book through the railway company directly whenever possible. It will save you money and you're also better informed in case of delays, cancellations, etc.

Per sj.se (for a random September date) : a private compartment for 2 people costs 1654 SEK (139€) while 2 beds in (gender-sepated) compartments would be 1660 SEK. To get that price add Interrail under discounts and enter your pass number (any number works).

Let me know if you don't see that price.

Thank you for the detailed answer! I now found out that i misunderstood the price of the Interrail reservation service, i thought it’s 55€ for 2 travellers (which would have been much cheaper than the SJ price) but it’s the price per person. So we decided to just take 2 seats.

Just for you information. At the moment, SJ's seating car haven't yet been approved by the Danish authorities so the seating cars are actually couchettes cars. This means that you might be able to lie down during the night even though you booked a seat. However, you need to bring your own pillow and blanket, and there's no ladder in the compartment. 

Hello,

I would like to make a reservation for a sleeping compartment for a couple (male and female) in the SJ night train from Hamburg to Stockholm.

Following your instructions, I manage to add my Interrail number pass through SJ company booking website, but I can either : 

1. Book “bed in sleeping compartment” and have to choose between Men or Women compartment for 1,660 SEK (Interrail fare)
2. Book “private sleeping compartment” for 3,710 SEK (it looks that the Interrail fare doesn’t apply)

By selecting OPTION 1, can my partner and I be in the same compartment or does it mean I have to book a private compartment (without Interrail fare) for my partner and I to be together in a gender-mixed cabin ? 

Thank you for your help !

You choose either male or female for both if you and then you must check that you get reservations in the same compartment. There are only 2 beds in the sleeping compartment on the SJ EN in 2nd class. The cost is 830 per person. 

Thank you for your helpful reply ! 
When I do so, I have seat 41 and seat 45 (in carriage 24) - but I cannot find the information whether seats 41 and 45 are both in the same compartment… Is there any chance you would know (where I can find) the information ? 

Many thanks

Those are in the same compartment. If the first number is the same, and the other number either is odd, like 11 and 15, or even, like 22 and 26, then it's the same compartment. 

Perfect, many thanks for your help!