Analyse this sentence for me.

[AUTOMOON]

Is it :
They are decorated with small round windows that remind you of ships, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.
Or:
They are decorated with small round windows that remind you of ships,bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

Second question ,here that
They are decorated with small round windows that remind you of ships, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.
What does this that refer? I mean which noun does it replace.
And what does the them refer to?

[susiedqq]

They are decorated with small round windows that remind
you of ships (some kind of punculation is needed here, either a semicolon ; or a dash - ) bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

or

They are decorated with small round windows that remind you of ships, with bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

[AUTOMOON]

You mean it's the first organisation.
Or, the sentence should have more" with".

Why should we add punculation there?

[Soup]

Aside from the words in bold, I can't seem to see a difference between your two sentences. (I may have missed your point.)

[1] They are decorated with small round windows that remind you of ships, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

OR

[2] They are decorated with small round windows that remind you of ships, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

It reads as if you are comparing the small round windows not only to portals (i.e., ship windows), but also to bent roofs and 20' high walls of glass, so you'll need to separate that by using punctuation as susiedqq has mentioned.

Try,

They are decorated with small round portal-like windows, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

As to your second question, "that" replaces or stands for either all of these: windows, roofs, and walls or just walls. It's hard to tell without more context.

The word "them" refers back to "They", but we don't know what 'They' refers to. Probably buildings.

[AUTOMOON]

[1] They are decorated with small round windows that remind you of ships, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

The first version, ships,bentroofs,and twenty-foot high walls of glass are all things reminded of by small round window.They are decorated with only small round windows.

[2] They are decorated with small round windows that remind you of ships, bent roofs and twenty-foot high walls of glass that make them special when compared with other architecture from the same period.

The second version, only ships are things reminded of by small round windows. And they(the buildings) are decorated not only small round windows but also bent roofs and twenty-foot high walls of glass.

By the way , what do you mean when you say:It reads as if you are comparing the small round windows not only to portals (i.e., ship windows), but also to bent roofs and 20' high walls of glass, so you'll need to separate that by using punctuation as susiedqq has mentioned.