Will magnets lose strength over time when coupled to another magnet?

My answer is, in general, no. Ferromagnetic materials usually, on a microscopic level, have domains in which the magnetic moments are all aligned in one direction. There is a famous picture from R. W. DeBlois that shows domains within a sample of nickel (the arrows indicate the domain orientation):

Kittel (Introduction to Solid State Physics) tells us that an external magnetic field can increase the magnetic moment of a specimen such as this by:

1. In weak fields, increasing the volume of domains favorably oriented with respect to the external field by shrinking those unfavorably oriented, and

2. In stronger fields, actually rotating the magnetization of domains.

Your magnets will already have a general N-S orientation meaning there are already large domains with that orientation. I am assuming in your design, you are coupling your magnets in a N-S/N-S order - in other words, you are not orienting them with opposing fields. So you may find that your magnets get stronger over time as the smaller domains grow and re-orient. I think as long as you stay below the Curie temperature, you will not see any decrease in magnetic strength.

Anyway, these are my thoughts.

Edit: I did look at a couple of magnet suppliers and they indicate an increase in strength when coupling two or more together. See question #22 in the link below. But they do not discuss the strength over time.

https://buymagnets.com/faq/#:~:text=Yes%2C%20stacking%20two%20or%20more,holding%20force%20is%20slightly%20reduced.

Magnets lose a very little fraction of their strength even if they are coupled to another magnet and are below the Curie temperature. But since the magnets are going to be used in a window frame which is opened and closed, there is mechanical stress which can cause high temperatures(reason at the end) and also wear and tear(speaking from personal experience, especially at rims) neodymium magnets are very susceptible to corrosion. So you need to take care of these factors.

(Sometimes while playing with neodymium discs I would let the magnets collide, a little bit of the magnet would get detached and even produce a spark in the process:)

If we are talking about human-life timescales, in other words any practical application then no they shouldn't. Unless there are other factors, such as mechanical wear, reorientation due to elevated temperatures, or constantly changing magnetic fields. However if you talk about extremely long theoretical timescales then magnets will lose their magnetism slowly, especially when there's a change in the field. So having them stay coupled should not affect them, pulling them off and putting them back millions and millions of times will decrease their strength. On extremely long timescales the magnetism will also be lost naturally but this takes so long that it's hard to even observe a loss in your lifetime (spontaneous random reorientation).

Again for any application in the real world you normally don't have to worry about this, especially when the magnets don't experience strong changing fields regularly.