Can two proteins sharing a few domains be considered homologous?
Homology means shared evolutionary ancestry. Sequence similarity is often used as a proxy for homology but inferences should be made with care. 

The similarity between two genes/proteins should not just be good but has to be statistically significant (metrics like E-value) for the two genes/proteins to be considered homologous.


  INFERRING HOMOLOGY FROM SIMILARITY
  
  The concept of homology – common evolutionary ancestry – is central to
  computational analyses of protein and DNA sequences, but the link
  between similarity and homology is often misunderstood. We infer
  homology when two sequences or structures share more similarity than
  would be expected by chance; when excess similarity is observed, the
  simplest explanation for that excess is that the two sequences did not
  arise independently, they arose from a common ancestor. Common
  ancestry explains excess similarity (other explanations require
  similar structures to arise independently); thus excess similarity
  implies common ancestry.
  
  However, homologous sequences do not always share significant sequence
  similarity; there are thousands of homologous protein alignments that
  are not significant, but are clearly homologous based on statistically
  significant structural similarity or strong sequence similarity to an
  intermediate sequence. Thus, when a similarity search finds a
  statistically significant match, we can confidently infer that the two
  sequences are homologous; but if no statistically significant match is
  found in a database, we cannot be certain that no homologs are
  present.
  
  Pearson, 2013


Members of a protein family are descendants of a common ancestor and are hence homologous. However, in the course of evolution they would have acquired new domains or reshuffled their domains such that their sequences are no longer similar. Proteins that have full length sequence similarity are called homeomorphic (Wu et al., 2004). Therefore, members of a protein family may be homologous but not homeomorphic. However, homeomorphic proteins can evolve independently and therefore may not be considered homologous. 

Identifying homologous proteins is, therefore, not a simple task. Machine learning algorithms are used for better identification of homologous proteins. Some of these algorithms are mentioned in the linked papers.

In general, global similarity, rather than local similarity should be considered for identifying homeomorphs. See What is the difference between local and global sequence alignments?