Fix node_depth

[YamLyubov]

Node depth was not working correctly for graphs with the following structure (decompose node in FEDOT)

Also update_node was not working correctly because only adding node to self._nodes does not add nodes predecessors to graph.nodes

[codecov-commenter]

Codecov Report

Merging #152 (f46f1a7) into main (9f8dfcd) will increase coverage by 0.14%.
The diff coverage is 96.66%.

@@            Coverage Diff             @@
##             main     #152      +/-   ##
==========================================
+ Coverage   73.84%   73.98%   +0.14%     
==========================================
  Files         129      129              
  Lines        7634     7649      +15     
==========================================
+ Hits         5637     5659      +22     
+ Misses       1997     1990       -7     

Impacted Files	Coverage Δ
golem/core/dag/graph_utils.py	97.29% <96.55%> (-0.62%)	⬇️
golem/core/dag/linked_graph.py	98.62% <100.00%> (ø)

... and 1 file with indirect coverage changes