A rule says that compound color adjectives are invariable.

Des chandails bleu marine.

J’ai vu des robes jaune citron.

Les feuilles de cet arbre sont rouge pâle.

Here are an exercise and some theory about color adjectives (in French only): http://www.ccdmd.qc.ca/media/ffiches_a_14Couleurs.pdf.
Also, a French Wiktionary page about it.

As for your second question, I think foncé applies to vert only, because

1. Jaune is plural, so it is a simple color adjective.
2. Otherwise I think the sentence would be Il n’y a que des habits jaune foncé et vert foncé or something.

In french, color adjectives are variables.

You can say

"Des pulls verts."

But ! If the color is also a noun, for example ‘orange’, it will be invariable.

"Des pulls orange."

But ! If the color is in two parts, it will be variable only if there is no dash between them, and only one the first word.

"Des pulls bleu-vert (no s)."

"Des pulls bleuS ciel (no s)."

So in your example, you should say :

"Il n’y a que des habits jaunes et verts foncé."

So in the first sentence, "foncé" can refer to "jaunes" or "verts" (but "vert foncé" is way more usual than "jaune foncé" so it is probably refering to "verts").

Sources : http://www.projet-voltaire.fr/blog/regle-orthographe/des-maillots-%C2%AB-orange-%C2%BB-ou-%C2%AB-oranges-%C2%BB

http://www.projet-voltaire.fr/blog/regle-orthographe/les-bleu-ciel-les-bleus-ciel-ou-les-bleus-ciels