I personally like making smaller subforms their own form as a pop up, but then you lose the ability to do master/child links which can be troublesome.
Parent/child links shouldn't be an issue. You filter the pop up for to the records matching the ID of the parent/source form to establish the parent/child link. - It's done differently from linking a sub form, but the effect is essentially the same.
As for the general design decision:
A pop up form puts additional cognitive and motorical load on the user.
Pop ups opening on top of the main form will disturb the visual picture of the user by covering an area of the main form. They might need repositioning for viewing information in the pop up and main form side by side. In contrast, multiple sub forms are in a fixed location. Even if the individual sub forms are very different from each other, the overall visual impression remains the same for the user.
Opening and closing a sub form requires two clicks to different locations on the screen, with the target area for the closing click being unknown before the pop is open (see above). Do not underestimate the cognitive load this implies for navigating the application!
In contrast, the click target area for switching to a different sub form is constant and visible immediately once the main form is visible.
Pop up forms are fairly flexible regarding design and size. Sub forms on the other hand must fit into the available space in the parent form and should have a visually uniform design with the main form, which limits the design options.
A major factor in deciding which option to use, should be the context in the application. If the "child" form displays additional information that should/must be seen in direct combination with the information in the main form, a sub form is usually the better choice.
However, if the information/action in the "child" forms is contextually only loosely connected to the main form, a pop up might be a better choice as it also visually emphasizes the context switch.
I'm not say one option is better than the other, but you should be aware of their effects on the UX.
PS: Here is a link to short
book review of About Face - The Essentials of Interaction Design, which I highly recommend in regards to UX design.